I normally start my transmission with the stock hims and spacing. I don't really file anything til I clean all bearings and relube them. I then put everything togethter and then use a old motor and run the transmission at 5v for 15 t0 20 minutes or so. Only lude on the gears is maybe some White Lightning chain lude for bicycles. I put a few drops on and wait a few minutes til dry. Then run my motor to break everything in.
Normally this makes everything pretty smooth and reasonably quiet. If it still feels tight after this I would then work on each trans half with some filing or space the trans cases up with the smallest shims I can find.