A833 trans alignment issue? Help

Unless that bellhousing was the numbers matching one for that engine block, it should be checked for runout. Max allowable is .005" IIRC. Any more and you may experience engagement/disengagement/shifting issues. You also may be just fine. But - it will depend on the clutch and the transmission. You had a clutch that worked. You replaced it. How easy did the trans come out and go in? Any chance the input shaft got pressure on it? Enough to bend or hurt the input bearing?
In this case, because it cleaned up with a new pilot bushing - I'd look very hard a tthe input shaft and bearing and I'd defintely check the bell alignment.