Here's my take on Rear wheel drive, manual transmissions...
Wear generally takes place in the easier to wear parts first, like the brass syncro rings. Generally, physical gear replacement isn't neccesary due to a bad syncro unless the syncronizing teeth on that gear are worn or missing. Also, most trans', I say most becaue I haven't seen all of them, do not require shimming of bearings to allow proper bearing pre-load or gear alignment. Manual tranny's do not have hardly any shaft endplay and do not require a certain amount and gears are pretty much set where they can go on the shafts due to the position of lock rings and splines.
What I would do for a trans rebuild....
Tear it down, replace all the brass parts and bearings no matter what. Inspect each gear individually for wear and replace as neccesary taking mileage into account. If it is a racing application, I would replace gears with hardened ones only if there becomes a problem with wearing out gears pre-maturely.
Again, this is just my take, I only have 5 years experience as a Ford mechanic, and am no longer doing that, but I do feel very confident in my abilities, the only question is, do You feel confident in my abilities?