Key communicator issue for a 5spd swap
 

I've done my search and I need help. I have a 2000 SC and planning to do a manual transmission swap. I've done some research but I overlooked info about the computer box. Will I have a problem with the key communicator if I swap it with a manual computer box? If so, what is the fix, if any? I hope I won't run with any more issues because I feel this swap may be more than I asked for.