Thanks for the detailed response!I did make sure they clicked completely. It looks like it's time to grab the mulitmeter and start going nuts. I know I am going to be so mad when it ends up being something dumb. If the Black w/ Green Stripe wire didn't make a perfect connection could that cause this whole issue? It seems from your explanation above it would not, but that really is the only thing I wasn't able to reverse to stock.
Looking at the schematic a bad connection on the black w/ Green Stripe should not cause the problems that you have for the reasons I stated above. To confirm this, I have an X-tre on mine so I disconnected the connector to the X-tre that goes back to the Black w/ green striped wire and left it off without putting the shorting (bypass) plug in it. This would simulate a totally cut wire. The bike worked normally with the exception that the temperature gauge went up to full hot level and stayed there.
I'm certain that there are other dash functions that wouldn't work correctly but the dash lights all come on and the fuel pump primes when in neutral. The bike started normally and the tachometer even worked. So cutting the Black w/ Green Stripe wire will not kill the whole bike. This is like having a totally failed X-tre which means if it does fail that it wont strand you, just that some dash functions wont work properly. This also confirms Jayhawks problem with the temp. gauge spiking up to the hot zone which would indicate a failing X-tre. I hope this help a bit as this rules out this being an X-tre problem. It's time to pull out the voltmeter and start looking for the missing voltage.
