This is why i now pay for tranny work
It could be anything from what side the spacers were placed on, to how the gears/forks were placed and held while putting the transmission together. The only local guy i know who touches them just puts them back together with stock shims. I've seen him build a few trannies from 2 broken ones and they all worked great but still felt like "old transmissions" slightly grinding and what not.
Maybe call Jon at TRE, he's honestly very helpfull about things like that, or at least he is when I call.
I helped his dad find some vintage motorcycle parts once years ago when i first met jon on the phone, so maybe that helped *shrugs* But either way he's a great guy and easy to talk to. I'm sure he'd give ya some hints at least.