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Thanks for the replies and thoughts!

I did have a couple of prop strikes, one of my favorite lakes was lower than normal and I ran it at an idle into mud trying to get back to the boat launch ramp... twice. Not one of my proudest moments.
I've not had a chance to run at full speed yet to assess vibration.
I noticed the run out after I took it out of the water and spun the prop by hand.
The next day I was warming it up for an oil change and the prop shaft was clearly bent, I removed the prop and measured just the shaft.
I'll check some more on the Hull truth forums... there was one post I saw that said .007 run out was max, that was on a higher HP merc though.

Here's a vid of the prop at idle before I started the straightening process: