Just thinking outside the box...
Have you considered doing all the work in a lathe with a four jaw chuck? I've seen many a crank built this way.
Yep, that's going to be a complex milling job. The coding for that would be way over my pay grade.
I do think I'd consider this approach. Ruff each throw out from the right and left side. One block of code for the left, mirror for the right. repeat for the next cylinder. This code would not be horribly complex. Then clean up the last few thou and do the bearings in a lathe.
Just more outside the box suggestions. Trying to avoid all the problems too long an endmill causes.