Brand new mainshaft, brand new 5/6 cluster. Whine is louder than ever now. Only in 5th and 6th though.

Thoughts on the cause?

 

You went from a loose 5-6 gear and worn-down mainshaft, to a reman mainshaft, lost a rear case bearing location surface, and who knows what else?

Thoughts are the same as if I were building it. Gonna have to see the parts inside. Whomever last built it may not have done so with an educated eye.