If you think it's coming from the left side, pull the stator cover off and check the flywheel. Just make sure it's tight.
Bike can run all day or intermittently with a loose flywheel. That's where I would start.
OK, if you run those the way they are shown, they will be wider than OEM by a couple inches per side.
The 3" offset will be towards the inside with the 6" offset on the outside.
So if you want to be wider in the rear, you will be good with those.
I would say that unless you're MXing this setup, I doubt you will see a ton of difference between a few clicks of compression/rebound.
I know DDQ probably pushes his suspension further than any of us here so maybe some direct PMs with him would be best.
As far as sag or ride height, set it where you feel comfortable on it. Go ride it. Make adjustments.
I doubt you're going to find a chart to tell you exactly where to set it because everyone uses their bikes for different things.