In the process of flushing some bad fuel out of the bike and trying to get it restarted I lost power to the fuel pump and plugs. All the other electrics work fine and the fuses next to batttery box are all ok. Any ideas?

 

Did you make sure that the wiring that runs from the fuel pump is connected to the female end that is under the tank (mine was zip tied to the frame I beleive). If you're sitting on the bike like you are riding it, the connector will be on your left side under the tank sort of by where the rear of the tank is. The wiring and the connector will be black. If it's plugged in, backprobe the fuel pump side of the wiring connector on the positive side with a digital volt/ohm meter (set to volts) and see if there is power going to the fuel pump. A test light may also work if you don't have a DVOM.