I bought a used 2012 last year and have put about 7500 miles on it. My experience is that some "vibes" seem to come and go, move around based on load, road, etc I have Givi hard bags, and if I run without the bags, I get some 4200 rpm buzz. Put the bags on, virtually nothing at 4200. I was surprised, but sure enough, the hard bag racks buzzed a bit without the bags attached. Makes sense when I think about it.
I also get a vibration at about 5200, but only if in 4th or 5th gear. Move up to 5500, or shift to 6th, smooths right out.
Put some foam grip puppies on your handlebars. It removed virtually all the handlebar buzz for me. (This was mostly at about 80-85 mph for handlebar buzz, slight but it bothered me) I "feel" the vibrations mostly in my butt or feet. Not very much, basically a smooth bike, with a few RPM spots of minor buzziness. Not enough of a bother to me to try to sort out. I do have engine guards as well, but Hepco Becker, not Givi.
Everything that was put on after the bike was made in Japan "may" be the cause of vibrations, according to smarter people than me. I bought mine with a ton of crap on it, so hard to say what might be the culprit. I have never ridden a stock Vstrom, just my well farkled one. I don't even know all the parts that have been swapped out!
As suggested, try running with/without some of the extra's, if it bothers you enough. Also, I notice when my chain needs some lube, I get more buzz. Make sure your chain is well lubed first, then do some testing.