Just got a well cared for Alumacraft 16.5. Its a great boat, but the electronics and trolling motor are dated and basic. I would like to upgrade to a fully integrated system eventually including a livescope/megalive. My frustration is figuring out all the pieces needed when looking at the trolling motor. Obviously I would prefer not dropping 5k all at once. I have a Helix 7 G2 I use for Ice and have no qualms using that for the next season, is there a MinKota trolling motor that would work with the autopilot & DI etc, that would be relatively easy to upgrade to Mega later if I get a new head unit. Or I am just looking at grabbing the Garmin 106SV, getting the Garmin motor and in a year or two add the live scope.

Many of the minnkota trolling motors are compatible with Humminbird graphs.  Your Helix 7 G2 is not going to be networkable however unless it's a G2N model.  
I currently have two Helix 7 G3N's on my boat along with an older power drive v2 24V trolling motor that I added a MSI transducer to.  It gets the job done but I'm looking to upgrade to a 36V trolling motor this winter.  Probaly a Terrova or Ultrex with the I-pilot link, and adding the ethernet hub to network both graphs and the trolling motor.  Might also add a talon too and that would also be networkable.  

It all comes down to how much you want to spend.  Personally, for live sonar, I feel that the garmin livescope 34 is hands down the top dog, but plenty of people run those as stand alone and have lowrance or birds for their 2D/SI/DI/mapping graphs.

Some reading to get you started if interested in Minnkota/Humminbird networking products

https://humminbird-help.johnsonoutdoors.com/hc/en-us/articles/4412814624791-Humminbird-Products-that-Network

https://minnkota.johnsonoutdoors.com/us/support/compatibility/link

Thanks, I ended up grabbing the Gamin 106SV that Bass Pro had on sale for Black Friday before seeing this. I am going to save up over the winter and grab the Garmin Force Kraken with 63 inch shaftand get in installed prior to ice out. I will have to add another battery as the electronics is only 12v now, so I guess thats 2 new batteries also since its a used lead acid, I dont just want to add a new one, and if I am upgrading my electronic batteries no reason not to get lithium except money. I will eventually upgrade to live when I get a good deal, but that will give me a SI/SI transducer on the trolling motor and transom.

The bird will just ride in the ice shuttle, for the foreseeable future.

You will be happy with that.  I sold all my bird's off my boat and have gone full garmin.  Ive been happy with them, and im still glad I switched to this day.  Everyone is different.  Ive had birds, lowrance, and garmin on my boat at some point.  For me, lowrance was my least preferred.  Lithium's are a huge game changer especially for TM's.  I went with Impulse.  If you do decide the go that route, do your research-I got a pretty good deal on the setup.  I was under 1k for a 60ah 24v with dedicated 24v charger shipped to my door.  10yr warranty and power is absolutely insane.