The only thing I can offer is to check wire connections on engine and tranny sensors. The ECM cuts spark and fuel during the shift and maybe it's not getting the feedback that the shift is complete.
Don't know which, but check the sensors one by one, pull off the connector, make sure its clean, if not, clean and put a little dielectric grease on.
Also, spark plug wires running near some of the sensor wires can cause bad information back to the ECM. Make sure no sensor wires are near the plug wires.
