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Brain overlord.....i would do a few google searches man. You are asking A LOT of questions some being pretty vague.

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While I'm not really that close to being ready to buy/build an AR, I do want to start making some preliminary decisions. I'm going to be looking for either one or two rifles for home defense use, I just have so many things floating around my head I'll just throw them out there. One will be for me, one for the wife. My wife has some slight damage in her right(strong) hand. It's mostly her middle, ring, and pinky fingers, she has close to 90% grip left in her thumb and fore-finger. I'm not sure yet if that will affect her ability to hold and shoot a rifle, or if she might need to learn to shoot left-handed(it would just be added to a list of things she is learning left-handed).

Barrel Length - In my mind, I don't imagine barrel length is going to be all that important for HD... I'm sure AR pistols probably have a significant drop in energy/speed/penetration, but I'm unaware of any ballistics testing comparing lengths. For HD, I'm thinking I would like to go quite short for weight and maneuverability, just not sure of any of the pitfalls associated with this. I just want to make absolutely sure that it maintains minimum penetration, and is fully reliable.

Are there issues with reliability under a certain length? not really. but since this is going to be your first AR go with 16in or a pinned 14.5.  
Are there issues with 'stopping power' or penetration under a certain length? no

Caliber - I've never shot a rifle other than a .22(*shame face*), so I really don't know anything about the recoil and sound levels of different calibers.

Are there any advantages for handgun-caliber variants over any of the more standard calibers? not really, depends on your applications
Are there calibers I would need to look out for in case of overpenetration?  not really sure what your asking.... dont by an ar10 or a .50bmg upper?
What calibers might be considered 'standard' for HD? 5.56 is fine, .300 blackout is nice too but this is your first AR, go with 5.56
What calibers might be best for having lower recoil and/or noise, while still maintaining penetration? 5.56 has a very low recoil
Also, are fragmenting effective, or is hollow-point the standard? i run green tip 62 grain. just because its what i shoot.

Supressor - From what I've seen on Sons of Guns, a good supressor can make a huge difference in sound levels.

Are there advantages to integrated over threaded? do you mean threaded vs qd? id go with a qd supressor.
Is there a higher risk of malfunction or under-penetration with a supressor? yes
Build/Order/Custom Order

Are there huge cost differences between buying a gun outright, getting something custom made, or putting it together myself?  you can save quite a bit building a rifle but theres nothing wrong with buying one either.
Would any of the modifications I might be considering here require custom work, or are there parts readily available for me to put it together?   by modifications i think you mean calibers and such, uppers are available online

Sights

What are considered the best sights for target acquisition at close ranges, that would work in full light, dim light, or darkness/dark+onboard light? almost everyone agrees troy sights are the best

I really appreciate the help... Got to learn what I can so I can become one of the helpers instead of the helpees one day :)

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no offence but im a little confused how you racked up over 1000 posts in a month and dont have an ar or this information. nonetheless im glad i could help.

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no offence but im a little confused how you racked up over 1000 posts in a month and dont have an ar or this information. nonetheless im glad i could help.

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Just glancing at a few of your questions, I would go with a 14.5 inch barrel with a pinned/welded flash suppressor. Provides shortest possible length without going NFA. 1/7 twist barrel so you can utilize all weights of ammunition. Flat top upper, throw either an Aimpoint or an EOTech optic on it, leaning towards Aimpoint due to extremely long battery life. No personal experience here with optics but someone who does will be along shortly. I would not pay to have an AR custom built. If you are handy with tools, or even if you can pay attention to a YouTube tutorial you can put one together yourself. Read some of the tacked FAQ threads here to answer some of your other questions.

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While I'm not really that close to being ready to buy/build an AR, I do want to start making some preliminary decisions. I'm going to be looking for either one or two rifles for home defense use, I just have so many things floating around my head I'll just throw them out there. One will be for me, one for the wife. My wife has some slight damage in her right(strong) hand. It's mostly her middle, ring, and pinky fingers, she has close to 90% grip left in her thumb and fore-finger. I'm not sure yet if that will affect her ability to hold and shoot a rifle, or if she might need to learn to shoot left-handed(it would just be added to a list of things she is learning left-handed).

Barrel Length - In my mind, I don't imagine barrel length is going to be all that important for HD... I'm sure AR pistols probably have a significant drop in energy/speed/penetration, but I'm unaware of any ballistics testing comparing lengths. For HD, I'm thinking I would like to go quite short for weight and maneuverability, just not sure of any of the pitfalls associated with this. I just want to make absolutely sure that it maintains minimum penetration, and is fully reliable.

Are there issues with reliability under a certain length?  With a Carbine gas system, I personally would not run anything smaller than 10.3".  I'm sure you know that you would need a $200 tax stamp to run anything shorter than a 16" barrel on a rifle.  A pistol AR can run whatever length you want and some of the pistol gas systems allow for extremely short barrels.  The advantage to a carbine gas system is that there are LOTS of options as far as handguards everything from cheap plastic drop ins to free floats.  There are also LOTS of makers of 10.3-12.5" barrels.

Are there issues with 'stopping power' or penetration under a certain length?  At close ranges I would not worry at all.  If it was me and I was looking for a do anything short barrel I'd go 12.5".  That can easily reach out to 100yrds as well as do the close work of a house.  The "Box of Truth" write ups that OldPainless does have proven that the .223 is a very solid performer for home defense.

Caliber - I've never shot a rifle other than a .22(*shame face*), so I really don't know anything about the recoil and sound levels of different calibers.

Are there any advantages for handgun-caliber variants over any of the more standard calibers? In My Opinion the cost is not worth the difference.  Right now standard uppers and lowers are pretty damn cheap, but when you start looking at caliber specific lowers and conversion pieces as well as the smaller amount of various caliber barrel makers the 5.56/.223 is a bargin.  Not to mention the plethera of cheap mags available.

Are there calibers I would need to look out for in case of overpenetration? If I remember it right, I have read that the pistol caliber rounds penetrate as much or more than a 5.56/.223 round.  Are you in a house or an apartment?

What calibers might be considered 'standard' for HD?  A good quality round like Hronady TAP would be my recommendation.

What calibers might be best for having lower recoil and/or noise, while still maintaining penetration?  Standard AR rounds are not that bad as far as recoil.  You can tune the recoil with the right buffer spring, buffer, bolt carrier, and muzzle device.  Problem is that the muzzle devices that make it shoot the softest also make it the loudest.  I'd look at something that redirects the noise forward like a Noveske KX3 or Troy claymore.   A 10.3" barrel with a KX3 is a nice combo.

Also, are fragmenting effective, or is hollow-point the standard?  I have my HD rifle set with Hornady 60grn Soft point.  I have not looked into any other rounds.

Supressor - From what I've seen on Sons of Guns, a good supressor can make a huge difference in sound levels.

Are there advantages to integrated over threaded? You are looking at tax stamp territory here.  Sons of guns rarely mentions you need to get BATF buy in ($200 tax stamp) to have one.  Also silencers will cost you around $500 on the low end and $3000 or more on the high end.  They do cut down on noise a LOT though not as quiet as the movies would make them out to be.

Is there a higher risk of malfunction or under-penetration with a supressor?  You have to have the right set up with the gas system to get a supessor to run 100%.  The easiest way to do this is just run an adjustable gas block on your barrel.

Build/Order/Custom Order

Are there huge cost differences between buying a gun outright, getting something custom made, or putting it together myself? I REALLY like building ARs.  I think I am up to around 12-13 builds under my belt including helping my brother with his and putting together mine.  The advantage is you can buy what you want the first time and not have to deal with selling off parts you did not want.  The cost of tools is not that bad at all and will pay for themselves with the very first AR you build.

Would any of the modifications I might be considering here require custom work, or are there parts readily available for me to put it together? Everything you have mentioned so far except the intergraded silencer can easily be done with the same tools you would need to build an AR.


Sights

What are considered the best sights for target acquisition at close ranges, that would work in full light, dim light, or darkness/dark+onboard light?  Do it right the first time and get an Aimpoint or Eotech.  Either the full size or the smaller versions of either.  In My Opinion for Home Defense I'd get a Aimpoint CompML3 for teh 5yr battery life so you can leave it on ALL THE TIME.  That or the Comp C3 with a 3yr battery life constant on.

I really appreciate the help... Got to learn what I can so I can become one of the helpers instead of the helpees one day :)

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I was thinking the same thing ... 1 k of posts in 1 month.  Seems that your time would be better spent reading and not posting, since the questions your asking are all answered in one form or another in this, or other, forums.  

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Keep this in mind....This is all MY OPINION and should not be considered gospel.  Others will chime in and throw their two cents in and you should look at everything that gets mentioned.

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5.56/.223 has very little felt recoil in a AR/M4 but either is loud as hell.  I have never used a suppressor but I do know that what is seen in movies is hog wash and I can't imagine that a suppressor will dampen the sound of a rifle round very well. I could be wrong, it's only a guess.

I find it hard to believe that any rifle round won't have over penetration issues. Again, I could be wrong.

I feel the best firearm one can have for home protection is a 12 gauge shotgun with bird shot, when faced with over penetration concerns. A 12ga kicks a hell of a lot worse than a .22 or a .223.

Buy a Mossberg 500 for HD and a Colt LE6920 for the range.

That's my honest opinion

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5.56/.223 has very little felt recoil in a AR/M4 but either is loud as hell.  I have never used a suppressor but I do know that what is seen in movies is hog wash and I can't imagine that a suppressor will dampen the sound of a rifle round very well. I could be wrong, it's only a guess.

I find it hard to believe that any rifle round won't have over penetration issues. Again, I could be wrong.

I feel the best firearm one can have for home protection is a 12 gauge shotgun with bird shot, when faced with over penetration concerns. A 12ga kicks a hell of a lot worse than a .22 or a .223.

Buy a Mossberg 500 for HD and a Colt LE6920 for the range.

That's my honest opinion

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12ga birdshot does not have the precision or stopping power a .223 will.  Buckshot has the stopping power but not the precision.  I have kids in my house and I know as long as i shoot over 4feet I am good.  I run a Aimpoint and a good light on my HD AR.  I practice drills at the range and I know my gun and my own limitations.  

As mention that would kick a lot harder and he is worried about his wife handling it.  manual of arms on a Ar is short and sweet....rack, flip safety, aim and shoot, shoot, shoot.  She has limited movement in one hand and safety, aim, shoot, pump, aim, shoot, pump, aim, shoot may be more than she needs to deal with.

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I suggest a 16 inch barrel with an A2 style flash hider on a Colt, Smith, Bushmaster, Remington or other name brand that stands behind their product. Smith and Wesson currently has the best warranty. Get one with an adjustable stock so it can fit your girlfriend, too. Call their customer service numbers before you buy and see who has a live person answering the phone issueing RA #'s. Buying from an FFL who can will ship the rifle in for service if needed is strongly recommended. Buy from Wally world and you are on your own, plus once Walmart drives the LGS out of business, do you think that their prices will stay so low? If you want a suppressor, be prepared to pay now and wait 6-12 months due to .gov approval processes. Go to an Appleseed shoot, CMP shoot, or NRA Basic Rifle course and bring the girlfriend with you.

I also suggest deleting the comment about her ex. Publicly expressing a desire to shoot people who are not presently a threat to anyone is ill-advised.

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Ah, I didn't mean it like that. He continually sends us death threats... if anyone ever enters our home to do us harm, it might as well be him so we can end it. If it's someone else, there will still be a pall over our heads.

I'll edit it though, thanks.

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5.56/.223 has very little felt recoil in a AR/M4 but either is loud as hell.  I have never used a suppressor but I do know that what is seen in movies is hog wash and I can't imagine that a suppressor will dampen the sound of a rifle round very well. I could be wrong, it's only a guess.





I find it hard to believe that any rifle round won't have over penetration issues. Again, I could be wrong.





I feel the best firearm one can have for home protection is a 12 gauge shotgun with bird shot, when faced with over penetration concerns. A 12ga kicks a hell of a lot worse than a .22 or a .223.





Buy a Mossberg 500 for HD and a Colt LE6920 for the range.





That's my honest opinion

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Knowing that there have been credible threats made, I should suggest a few more things.

Report the threats. If reports have been made, follow up and be sure to report any additional threats. Get restraining orders against her ex. Stop dithering about what the perfect HD firearm is and as soon as you have some coin, buy something reliable and start practicing with it. A 20 gauge 870 can be had for very little and your wife can learn to shoot it. They make reduced recoil slugs. Many instructors are now offering free defense training to anyone who has a protective order against someone. If you get an order and need help lining up training, let me know and I will find someone in your area who will make time to train you guys sooner, rather than later.

People who choose victims based upon past relationships are often the hardest assailants to stop. They cannot be disuaded by consequences and are rarely rational anyway. Please get yourselves prepared.

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Knowing that there have been credible threats made, I should suggest a few more things.



Report the threats. If reports have been made, follow up and be sure to report any additional threats. Get restraining orders against her ex. Stop dithering about what the perfect HD firearm is and as soon as you have some coin, buy something reliable and start practicing with it. A 20 gauge 870 can be had for very little and your wife can learn to shoot it. They make reduced recoil slugs. Many instructors are now offering free defense training to anyone who has a protective order against someone. If you get an order and need help lining up training, let me know and I will find someone in your area who will make time to train you guys sooner, rather than later.



People who choose victims based upon past relationships are often the hardest assailants to stop. They cannot be disuaded by consequences and are rarely rational anyway. Please get yourselves prepared.

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OP, get yourself a 14.5" (flash hider pinned so it hits 16") carbine gas rifle from Palmetto State Armory, Bravo Company, or Spike's Tactical.  Practice with it as is.  If you still want a shorter barrel, get the ball rolling on a SBR for that receiver.  It takes quite awhile for the paperwork and tax stamp to clear.  When you do get your stamp, figure out what length you want and send your upper to a smith and have it cut down to the length you want.

This way you can practice with the actual rifle and learn it's manual of arms.  Hell maybe you will figure out you don't need the SBR.  Any of those makers will give you a solid platform.  This will also allow you to figure out what optic and light you want.