I think I figured it out. And of course it's not one thing. There are several factors contributing and one pretty big mess up. At this point it's almost gone, hardly noticible. 

These are the things I've be adjusting

• Springs – biggest factor. They were crazy stiff, but are now replaced with Progressive original weight springs
• Pre-load spacer. Smaller by half
• fresh fork oil (went with 10 weight - what Duncan has and suggests)
• Wheel balance. Was a little odd, but ended up having Duncan's Beemers check it
• Good tires centered on the rim
• Tire pressure on the lower side (around 32lbs) 
• Steering head bearings. I've had trouble getting these to stay tight. As it loosens up the vibration is worse (new bearings)
• I don't think the small dings in the wheel are a problem. It would be nice to have a perfect wheel, but it's traveled 47,000 miles in New England... I think the tire/shocks now absorb the very minor run out. 

So thank you all for the suggestions and advice. 

Ride safe, ride often. Cheers

Glad to hear. Wonder how those springs got in the bike?!!