Well, for those who might be in the least bit interested:
The rubber washers between the tree and the windshield bracket really didn't do that much that I can tell, probably because the bolt still directly bolts into the tree and transmits vibration directly.
The rubber washers between the shield mount and the lowers, slightly more success and reduced vibration. Also the increased silicone, extra radio rear strap bolt, and foam block beneath the radio seems to be holding up. I can now listen to the radio again at 75 mph, so something clearly worked.
Overall though there is still too much vibration for my comfort in the whole setup, so I have a feeling I'll be chasing down loosened screws every month or so until I fix the vibration problem at the source. Small squeaks, vibrations, and rattles drive me up a wall, and I seem to have purchased a set up that is nothing but. Should have gone HD fairing?
Time will tell.