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On gears, look for signs of rust pitted or chipped teeth and uneven wear or steps on the drive faces of each tooth. On the counter shaft cluster see how much end play it has. On the 2nd/high gear look for condition of the engagement dogs where the gear fits up to the input shaft for 1:1 drive. They shouldn't have too much wear and no damage on the engagement surfaces. Wear of gears on shafts(play) should be scrutinized. Condition of the bearing surfaces of the input shaft and main shaft should be checked. The roller bearing that fits in there is one that some folks have been having problems with as well as the two for the cluster. The bearing and journal surfaces on the counter shaft & inside the cluster shaft for those bearings should be checked as well.
I've known folks that put together the trans with gears that have some pits and decent used but still serviceable bearings and such and have gotten away with it but a person just has to use their best judgment on what they want to get back out of the work put in. A lot more is available now than there was 30 or 40 years ago. I'd be looking for the best caged rollers available. Some of the Asian stuff doesn't hold up well so check with the sources that back their parts or re-use good originals. Just make sure they are good. Check this thread on specific bearings.
https://www.fordbarn.com/forum/showthread.php?t=298125