My bike is almost working after replacing the harness but I have a problem.
I don't have power going to the fuel pump. It looks like the ignition modual
isn't sending power to the fuel injection relay. I though at first it might not
be plugged in all the way (hard to get to under there). Any idea's? It could
have fried when the harness shorted. I'm having trouble getting it open. Is
there anything I can change inside? Thanks for any help!

Do you got power to the FI relay coil?
Does your starter turn over?
Other symptoms occurring?

Well everything else is working now. The starter works, but I disconnected it to check the
fuel pump power. The power is not getting to the coil on the fuel injection relay. It comes
directly from the injection computer. Not sure how to check it out?

The power to the FI relay coil comes from the kill switch,
the ignition ECU grounds the coil.

The kill switch could also be the reason to your clutch switch problem, same source
Since the starter working, you got power to parts of the circuit that the kill switch feeds...so if you ain`t got power to the FI relay coil...the problem must be in the wiring.

The kill switch also feeds the coils......

Well I see the dash turn on and off with the kill switch so I believe that is OK. I didn't change the
switches on that side and found a loop back that was burned up. I fixed that but maybe one connection
is bad at that junction. Time to get the deoxit out. Thanks for the tip that the Ignition module supply's
ground!

Since you got power to the instruments, I suggest that you check the wires at the frontmost connector at fuse #1.

It should be two yellow/green wires, one coming from the kill switch, the other going to the FI relay coil.

The instruments is connected after the fuse.