starting issues

I purchased a 1998 tlr for my daughter, it needed a rear head so I removed the engine and replaced the head with a used head from a 1998 tls. the guy I purchased the bike from had all the wiring disconnected and there were some extra wiring for the coils that I assume was the mod for the coils...

So my tlr has never started that great ever since i put this motor in six months ago ive always gotten a code for rear coil signal but coil was in spec still got a new one plus new caps no change ive looked over my wires hundreds oftimes. Now my bike is really taking a long time to start like 10...