Man I've been working on a kilowatt for a while now. Stroked 460 billet everything through a 780 torque converter. Hydraulic disc brakes front and rear with a billet rack and pinion.
Another battery idea that I caught from the same guy is a drill battery, that's what he used very small lightweight and compact! There's even a few companies out there that build billet battery mounts to accommodate them. I personally am using a battery very similar to yours from a company...
There's a guy on Instagram that went the MSD route, he had the same issue and I believe you're hunch is correct. He contacted ARC and they built him a flywheel with the correct magnet. I don't know if I was supposed to mention what I have mentioned but I did LOL.