The timken bearings are pretty easy to see if bad. Pitting,metal flaked out etc. These are very common to find flaked out from banging around with too much end play. The ball bearings are harder to see inside of but try and look at them and clean them up good and see if they feel smooth and not real loose.
The outer most one on the RH side in the reduction cover,the live pto idler gear ones,and the one in the center of the sliding gear shaft that sets into the input shaft seem to me to of been the most prone to failure on the ones I had apart. Sound like you could of had ALOT of metal particals floating around in that oil if you had 4 gears bad ?