I found this info in this thread on Pirate basically you want to check the tc input shaft before you go cramming the cheap deal of a TC into an application other than a 4speed L43 though commonly thought not all RF1A TC's are created equal
Pretty common symptom when an early input is used. The input from a 79 or 80 t case has an input that is not good to use unless you grind it down or replace it. Here is a pic of the one you want grind on or stay away from.
Check Dave's picture above. All inputs are tapered at the end, but the inputs found behind a L43 4-speed (20R applications only) have an enlarged spline collar that mates with the fully splined transmission output coupler. When the next-generation L-series transmissions were introduced (L45/50/52), the output coupler was redesigned with a 1/2" counterbore (with no splines). This helps the transfer case input shaft find the transmission output coupler during assembly on the production line.
Toyota was probably damaging transmission output seals with that enlarged spline collar and were looking for a way to improve the design. We believe the 2nd generation 21-spline inputs are made from better metal therefore the strength of the splines were no longer needed, however we have not proved this theory. Another theory could be that Toyota wanted to include a "fuse" in the drivetrain.
Here is a picture of the L43-style transfer case input I installed behind a Marlin Crawler W56A-HD 5-spd trans: