If you have the transmission out, then I'd definitely recommend opening it up to replace the shift return spring if nothing else. Got an email from a fellow down in TN the other day wondering how much work it was to replace the return spring - he had the clutch replaced just a week earlier...
When I built "Barney" http://thisoldtractor.com/gtbender/p...arney_blog.htm
I used a presumed good transmission. Upon inspection, it was found that the input shaft would only turn so far then "crunch", same with the output shaft. Opened it up and found rusted bearings and 2-3 "sliding muff".
I don't have the time (or money) to do things over, so I try my best to do everything right the first time.