I found where that ground wire goes. It connects from the ground under the tank to the ground on the gear box. I found another thread on here that showed the exact wire and where it goes.
I've now got all the electrical hooked up and replaced all the fuses with new ones. All the dash lights work, indicators work, brake light works, and headlight works.
I followed the steps here (
http://www.motobrick.com/index.php/topic,3781.0.html) to install the fuel injectors and to make sure that they don't leak (no leaks detected). I can hear the fuel pump working and I can see fuel returning to the tank.
I removed the spark plugs, cleaned and checked the gaps. I checked for spark on each by grounding it to the engine and pushing the start button. Each plug has spark.
I tried to start the bike but it won's fire. I pulled the #1 spark plug and it was wet with fuel.
So now I have to solve my no start problem. Off to search the forum for solutions.