I got the Intruder put back together and running. Put in new seals (old ones completely shot) pistons,rings etc.
In the Kawasaki repair manual they recommend after a complete tear down to run 5 gallons of premix at 40:1 through it. I put clear lines on the injector pump, got all the lines bled and have oil going to the motor from the pump. The thing Kawasaki is not clear about is if you should be running the premix and the injector or just run the premix until that is gone and then put oil in the reservoir and switch to injectors only.
Seems to me if you are running premix and the injectors, it is going to be quite rich for a while.