After a flush I measured the amount of water that comes out the fill tube during a flush and it is over half a gallon.  So add that to the water that gets dumped into the bowl during a flush and this just shouldnt be a problem.  The fill tube is solidly attached to the overflow tube and I have verified that 100% of the water from the fill tube is going down the overfill tube.  I have no idea where all that water is going; its not on the floor and its not in the bowl so somehow I guess its going down the sewer?

Now, I did notice that where the tank sits onto the bowl platform, that inside where the bowl receives the tank water during a flush, right there in the bowl there does seem to be 2 different ways for water to run, does one of those paths just go straight to the sewer, bypassing the bowl?  If so then I guess all my water from the fill tube going down the overflow tube could somehow be directing a lot of that water from the fill tube straight into the sewer?  Just a guess?

So thats where we're at now.  I had a leaking flapper so I got the "Fluidmaster Performax 3 in. Universal High Performance Everything Toilet Repair Kit with Install Tools" from Home Depot and installing it was a breeze.  But after reading 100% of the instructions and adjusting every possible setting I still need help adjusting the water level in the lower bowl as now there is very little water in the bowl after a flush, much less than before I replaced the flapper.  I've looked at all the instructions and have adjusted every setting so that the fill valve is open for a very long time during a flush, and have also turned up the refill tube adjustment to the max possible volume of water.

Where is the fill tube water going?

I could explain, but the better thing would be just to tell you to YouTube it.

all that I've already done, they say to

1. make the fill tube run longer by raising the water level in the tank so that more time is needed to fill the tank such that the fill tube runs longer
2. increase the volume of water from the fill tube
3. make sure all the water from the fill tube goes down the overflow tube
4. make sure the tank drains completely for a flush

I've done all that, I cant figure out what Im missing though

Continuing to siphon through the drain due to a clogged vent?

@Bulldog8 do you mean a vent leaving the home?  Or some kind of venting within the toilet?
(this is a new issue after replacing the guts)

Heres a pic of the bottom of the tank with the flapper removed, showing the 2 parts of the bowl underneath



so the water that goes down that smaller sect to the left there goes to the jets that fill the bowl up after the flapper closes.  The larger part on the right seems the main flush/dump path.
I manually tried to put a ton of water down either side, and couldnt really raise the bowls water level very much no matter how much I put in.

That flush valve is backwards from what is standard.  Could this cause your problem? Not sure, but it stands to reason that the flow of the flush will start from the wrong side.

Try some food coloring or soy sauce so you can figure out where the fill water goes in those two spots.

Neither are likely direct draining to sewer but the fill could be hard to spot.

Low Fill could be a flapper open time thing, fill tube height, float level setting.

Also put some cleaner in the bowl and plunge it good. Paper or debris hanging on the inside of the trap can wick water out of the bowl.

My wild ass guess would be that your using too much water and it's causing the water in the bowl to siphon down the drain. If you have ever dumped a bucket of water down the toilet it does the same thing.

Fill the bowl manually with water.  Does it stay at normal height?

no.  it never seems to fill up, regardlessly of how slow I try to pour  its like magic.  i need to go get a plunger we must have lost ours in the move

Yes I was referring to the vent leaving the home. The vent breaks the suction that causes siphoning, but is not likely the cause if the problem started after replacing the fill valve.

However, if the old fill valve did not flow very well, it could have masked a vent issue. If the new fill valve moves a lot more water you could now see a siphoning problem that wasn't noticeable with a lower flow valve.

Did you figure it out?  Since it won't fill by pouring water in, it sounds like you might have a broken toilet casting.  Not sure how that could have happened by replacing the flapper, but the height of the weir (highest point of the p-trap built into the toilet) is what regulates the height of the bowl water.

Pull the toilet and look underneath where they cold patched the bottom of the trap. American Standard had an issue with this years ago.