At the risk of repeating my earlier sentiment (really not trying to beat a dead horse here), why would you even care about the degree of hardware changes? Is it worth saving it?
The old design had HV and LV mixed up all over the place, reference voltages traversing boards with unshielded cabling terminated on chinsy 0.1" headers that don't even lock into place, or offer insertion polarity protection... Not to even speak of the questionable software architecture...
You wanna do the community a favor? Chuck the whole thing and start over. ;-) A fair (and perfectly workable) compromise would entail re-using the expensive bits (IGBTs, inductors, etc.) since those seem to be chosen with some degree of engineering effort behind them.
Existing users might like to retain their display, but if it were my design, I would make the box CAN bus operated with maybe a serial programming port, and offer an optional programmer with the LCD and all, which communicates over CAN and can be located anywhere. Then the charger can hang out in the trunk, hood, or wherever. Controls in the dash, glove box, or a plug-in hand-held unit.
While I'm throwing around unsolicited opinions... I really don't think Arduino is the platform to go with here. Yes, it lowers the barrier to entry for contributing coders, but ... and I'm sorry if this comes across snooty ... if your contributors can't figure out how to use a real dev environment and/or toolchain, do they have any business writing code that is responsible for containing the fury within a multi-hundred volt Li-Ion battery pack, with charging currents of 20-100A? This thing isn't a toy, you know? Maybe that's not fair, but I like the idea of knowing my firmware is written by someone that knows how to handle a pointer.
Outside of Arduino-land, Atmel AVRs are a perfectly fine chip, if not a little pricey for what you get. Their docs are fantastic. I'm not much of a PIC fan - I kinda feel like the only reason to use them for new work is if your dev team have been using them for 20 years and can't justify learning a new platform. Although, they have a good history of long-term availability. Admittedly, this is probably just personal bias, without any substantial meat to the argument.

They work and work well. Dev tools and licensing stuff sucks though.
IMO, the new fleet of ARM Cortex chips is where it's at. But, ultimately, you can get the job done with an 8-bit CPU, if you're more comfortable with look-up tables and fixed-point math than fast 32-bit int and floating-point arithmetic calculated on-the-fly.
Just my 2c, for what little that might be worth. Carry on.