If the IMA light is out, the car recognizes the battery. The BCM just has no idea of its state of charge as resting voltage does not correlate to state of charge, so it shows zero. If the IMA light is still on, you have other problems.
There are no issues with shoving a fully charged pack in a car. If you can, it's best to let the voltage stabilize over 30-60 minutes (maybe overnight), but two weeks is excessive.
Disconnect 12V for 30 seconds. Reconnect. Start and rev to 3500rpm and hold until you read full bars. You will need to drive it as you will show DTC not ready when you go to emissions, which will be the case no matter how you reset the codes.
Given the atrocious state of imbalance your as-removed testing showed, I expect any improvement will be temporary and you will need regular grid charging/discharging.
Did you confirm the sticks could sustain a 100A load for 10 seconds and remain above 5.4V?
NiMH voltages don't mean a lot. They can give indications, but there is no objective relationship due to other variables.
You have already invested a lot of time in this project. I have done the same over 2 HCH1 packs and 6 HCH2 packs. If you want to maximize the value for your efforts, next time you are looking to re-balance your pack, do it over a weekend with pack grid charging and deep discharging to < 1V (yes, 1V for the entire pack) with 2X 100W bulbs in series. Yes, you will reverse most of the cells. No, it won't hurt them (will happen at current under 1A). Yes, you have already reversed at least 1 cell per stick at far higher current when discharging to 0.8V/cell. I have watched it happen at even lower currents. The speed of weak cell depletion and polarity reversal under high/medium load when discharging to <1V/cell is astounding.
There is a mountain of evidence of others (including me) that have done this with very favorable results. My capacity recovery has been 20-25% for a given load without exception.
Here is a before and after comparison between 2 discharges to 132V on HCH2 packs. First one is following a topping grid charge to peak voltage at 350mA. The discharge was continued to under 2V followed by a topping grid charge to peak voltage at 350mA. The second data set is the same discharge (500W halogen) to 1V/cell:
https://docs.google.com/spreadsheets...it?usp=sharing