Thanks, yes I am using jis but had to order bigger sizes. The new bits and an impact drill got them out with no issue.
After removing the drum and shift forks, damage became clear.
Drum had a good piece of a corner sheared off. One fork also had a deep groove, another showed cuts.
With all the debris inside the engine, the oil pump now grinds and has grooves. All of the above will be replaced.
One fork is on national backorder and I had to order from japan. Will take a bit to get here.
I cleaned the bottom case and it's ready for assembly once I have everything.
I'm glad I'm doing all of this. I'm sure the engine would have failed at some point.