Hey All,
Is it possible for either the starter switch or the start cicuit to be sending a signal somehow to the EFI # 4 teerminal even after the engine is running? I only thought of this after exhausting all the other possibilities and testing...

Hi there, when you press the starter switch while the engine is runing the FI will enrich the mixture. If you do so at idle rpms will rise, this is a way to test that idle mixture is not over rich wen you dont have a Co tester.
Best regards
JAP

I installed a known good AFM and still no luck but as I was about to give up I was moving things around a bit and the engine smoothed out and ran like a brand new bike. I took it for a long ride and the performance couldn't have been better. I parked in the garage and thought I would start it hot and VIOLA the darn thing started it's act all over again..... putt putt putt and heavy smoke!!!

Though you didn't say what you moved around a bit, definately sounds like a poor electrical connection. So now you are very close...