I am enjoying your thread--and learning quite a bit. I have two '81 IT465s I am combining into one. I have a new top end--piston and freshly bored matched cylinder. I also have some new wiring, new bearings everywhere, new DG exhaust system, new bars, new tires, new cables, new brakes. In short, a nice project ready to put together and try out.
My biggest dilemma with the IT465 is that neither of my cases will work without some repair and maybe machining. The better of the cases has a hole between the tranny and the crankcase.The other case is shattered at the kickstarter shaft (lots of abuse there from energetic POs, I fear). I recognize some of the flaws in your cases as similar to my own,
Your photos and research have shown me my cases are about par for the course and not unusually damaged. I am also learning what to look for as I put everything back together.
My best course of action, though, might be to purchase a set of cases in good condition and bin what I have. I have plenty of tranny gears in good shape so even a worn out gearbox won't be a deal breaker for me.
Thank you for taking the time to document your YZ project