Installed the HD security system on my 2002 RKC, ran through the programing and installed personal code. The bike starts but will not run any suggestions? Modifications to the bike include stage II, pipes, stock ECM flash, and a power commancer.
You mentioned it "starts" but does not run. I assume you mean the starter turns but the motor doesn't start, right? The only way it could be your security system is if the "armed" (flashing red key) led light is still illuminated on your speedo. Lots of folks having trouble with the disarm function (double click) on the key fob.
Remove power from it, either acc, ign and security fuses or preferably a battery cable and go at least twice thru the initialization and then try and program it and the remotes according to instructions. The initialization is designed not to work the first time.
If that doesn't work you need to go thru the password learning procedure to match the ECM and TSSM password. It can be done manually, it just takes a while.
Another fellow had the same thing HERE, but keep in mind that his situation was completely different because his alarm worked at one time and the way I understand your post yours never did.
If you get too confused you can just plug the old TSM back in, ride the bike to the dealer, plug the TSSM back in, and have him match passwords with the scanalizer. If they are halfway fair it should be less then one hours labor.