Where can I find a manual transmission for a 1994 3.1L beretta?

1994 3100 engines (and all 3100 engines, for that matter) never came mated to a 5-speed from GM. You will need to make all necessary modifications and installation yourself. Any 5-speed from an earlier V6 Beretta/Corsica (1988-1993 2.8L or 3.1L MPFI), Cavalier/Sunbird, Grand Prix, etc. will bolt up. I recommend a Getrag, if you can find one in a yard. Note: You will have issues with the SES/Check Engine light coming on, due to the ECM no longer finding the electronic component of the automatic transmission. This cannot be cleared on a 1994 or 1995 Beretta.