Update:
We've reinstalled the stock friction and slip plates and did the best we could to return the problem back to the original state when the issue was very minor. The same issue of lurching forward with the clutch pulled in is just as bad even in the original configuration.
That was actually an issue we had the very first time we put it back together. When the pressure plate is misaligned, the bike will not go into gear at all. So we tore back into it, made sure the plate was lined up correctly, and tested the function before putting the cover back on.
So the...
I am the brother in question. The push rod never came out, so its still there. We double checked the presence of the ball bearing, which also was not removed in the first place. We have checked diagrams in the service manual and are confident all components are present.
Any other...