You are correct, you will need 3.5" Rox risers to clear the Scott's damper. With 2" Rox risers, I had to angle them forward to have room for the Scott's. That was no good at all, which was why I got the 3.5" Rox's.
I'm not sure I understand what you want to do re: risers. Putting the handlebars on 3.5" risers will raise them substantially vs. stock position. It will also move them forward or backward, depending on how you set them. You will need +2" brake and clutch lines. If you like the stock handlebar position, don't install risers.
Fatter bars will flex less, yes. As long as they taper back to 7/8" at the ends, you can still mount all the equipment. Aluminum bars will have a thicker wall, so you'll need to modify or replace the bar-end weights.
I do not have the mirror movement issue you have when going over bumps. My bars do not vibrate in that situation either. Maybe your mirror mounts are loose, or something else is?
I had a look - yep, stock rubber is in the handlebar mounts on my 2007. Never knew that was there. The bars feel solid. I definitely would not remove the rubber or try for metal-on-metal mounting. Then you will feel every bump, crevice, and irregularity in anything you ride over, as well as every bit of vibration caused by slightly uneven front tire wear. That would suck badly on the highway.
The Scott's will not damp front wheel/other small-displacement vibrations. It can only affect large-scale steering movements, or forces trying to cause large steering movements.
tl;dr: don't install risers if you like the bars where they are. Don't remove the rubber from the handlebar mounts, it will make things worse. Yes to the fatter handlebars.
Hope this helps.
2007 Vee with too many farkles and 50k+ (s)miles
Last edited by DesertBike; 06-14-2019 at 11:37 AM.