The shift gates were checked during the alignment of the 2 linkage rods and are good. The engine/transmission was purchased as a unit that was still bolted together (and had not been unbolted in a long time, judging by the layer of crud on them), and both were working fine when pulled from the other truck last year. It was well covered, but was still stored outside for about a year. The output shaft turns easily by hand when the clutch pedal is depressed, and also turns easily if the shifter is in the neutral position with the clutch pedal not depressed. I'm not quite sure what to try next!