My 901 sideshift seemed to work fine, shifted smooth no grinding (unless you are too agressive shifting). The only problem I would have is that sometimes it would get "Stuck" in 4th gear. Sometimes it took considerable force to pull it out. It happened randomly with no apparent pattern, most of the time it shifted fine in and out of 4th.

The shift linkage and bushings look like they are fairly recent, everything seemed nice and tight and moved freely.

Is this an indicator of an internal problem with the transmission, or do you guys think it is linkage related?

make sure you have enough, fresh, proper-spec transmission oil. i haven't had this problem, but when it has come up before, it has frequently been solved by changing to a good quality oil.

cheaper and easier to try, first, before diving into transmission internals...

did you replace your engine and tranny mounts? maybe one or more of them is messed up.