As there were two different transaxles used for the vehicle, depending on what engine you have, it could be any number of things.
If yours is a 4speed OD, 41TE, the TCM (Transaxle Control Module) could be directing the transaxle into "limp-in " mode, which allows only P, N, R, and 2nd gear operation, due to a fault code being detected. This can be a result of an electrical or mechanical issue, and a fault code will be stored in the TCM's memory. Unfortunately the TCM has to be scanned with a diagnostic tool to retrieve the code. Most common electrical sensor issue is either the input or output speed sensors.
As for the 3 speed 31TH, many problems associated with poor down shifting can be caused by sticky governor valves, mainly caused by internal wear, damage to bearings, bushings, debris from wear. I would verify proper throttle pressure adjustment, and correct assembly of the linkage (a missing return spring on the throttle lever linkage can cause delayed, erratic or no downshift).