This is a very subjective thing. Some people are bothered by vibration that other folks never seem to notice.
I've put 15K on my Vegas in the last 2 years. Based on that experience:
o The mirrors will not vibrate if the mounts are tight and adjusted properly (mirror should be in the middle of the adjustment range, not pulled over as far at it will go in any direction).
o The handlebars are never an issue since I've added my ISO grips.
o When not wearing my riding boots, I do notice a little vibration in the foot pegs. Never an issue when I have my boots on, which is most of the time. My riding buddy has a Kingpin and never feels any vibration with the running boards.
o Tires can be an issue. Double check the inflation (I run 38 front and 40 rear). Low inflation pressure will cause vibration on my bike. If the tires are inflated properly and still vibrate, have the balance checked. With my Avon Venoms, I'm good to well over a hundred per (on the race track of course) with no vibration to speak of.
Good luck getting it sorted out!