Got it back together! I ended up pulling the rotor and flywheel again. I couldn't find anything that would make it off, but after reinstalling it I didn't find any runout like I did before. I adjusted the mag pickup to 3.16 volts. It has to be only 1/4 to 1/2 turn out to achieve that. I may take one off of a parts machine and swap them at some point. Pickup is damaged but still works.
Often, runout problems are solved just like you did it. Simply re do the installation. With turbines, it's much more complicated. Good work!
in the long run, it will pay you to re adjust the mag pickup to 3 volts, and no higher. Sooner or later, dirt, grease, oil and metal chips can foul the end of the pickup. It helps to have the tip farther away. And there is no chance of it grinding again. And if it works, it's good enough to use, so don't replace it, just turn it a hair farther out until you get 3 volts.
I only fired the unit for 5 minutes after getting it back together. It seems like it is running a whole lot smoother. I will finish the sheet metal and do another load test on it before I call it good. I've got to dig out a parts machine to get a volt gauge off of before I run this thing very much