I would have sworn that they had ball bearings, anyway I should think you could fit some form of thrust bearing, maybe even bronze, it probably would need a bit of machining of the c/case, but not having seen it , couldn't say for sure if it's possible.
The small end bush might be a slight handicap and would probably be ok if it had a good sized lubrication hole on the small end eye, but it maybe could be replaced with a needle roller ( if the pin is hard enough).
The built up crank is very strong looking one, and in my opinion is a bonus, heavier but stronger than the single sided overhung type. The rear part of the shaft could be easily cut off. the seal taken out and be replaced by a blanking disk.
To convert to ball bearings would require machining out housings in the crankcase, and again it could be done ( with access to proper facilities), providing of course that there is enough "meat" in the cases.

I haven't seen the transfer ports so don't know if they are good for power. I do see your point about magneto etc., could be a challenge!

Maybe if I can find the time I'll tear mine down and check it out

Someone, somewhere, must have done this conversion with success, maybe they will see this and give you some good tips.
Good luck.