There are so many unknowns here it is hard to diagnose from 500 miles away... And I know exactly what you mean feeling silly taking it to the dealer -- with my luck it would be smooth as silk and I'd be unable to illustrate the problem to him. Like going to the Doctor and the pain is gone...
I do not know your situation and what kinds of tools and gadgets you have access to but here is a thought:
1) The bad vibration state of affairs (call it Bad versus Good for shortening this discussion) -- when it is 'bad' one would think you have one cylinder not 'firing' properly. I could guess a faulty injector or some issue in the high pressure side of the fuel system leading to that one cylinder. On a brand new machine you as owner should not go digging even if you have the background/capability to do so.
2) Lets hypothesize one cylinder is missing for whatever reason. Bad fuel from that first fill-up you mentioned way back, a bad injector from the factory that has a defect, who knows.
3) If you have access/own/or just go buy one of the hand-held infra-red thermometers [Amazon dot com has them in the $13 price range and your local stores carry various versions...] use one of those as follows:
-- Get familiar with the normal operation of the "temperature at a distance" thermometers. Try it out, get repeatable readings on various things warm/hot etc. How far away you hold it, how it acts, etc.
-- Measure the temperature of your cylinder head very close the base of each injector with the engine cold and not running -- all the same of course. Better be.
-- Run the engine a while and observe the rising temperature the longer it runs up to some stable final operating temperature.
-- During that run-up sequence, go from cylinder to cylinder, expecting to see each one in the same temperature ballpark. Keep doing that until the engine is finally hot at its normal operating point.
In that sequence/process IF YOU HAVE THE BAD Vibration, then I suspect you will also have one cylinder head top area cooler than the other two. If you catch it with BAD vibes AND find which cylinder is the "cool" one then that tells you which one has the problem.
Keep in mind that, over too much time, (if you let it sit there and run for half an hour) the heat will conduct all along the cylinder head and you might no longer be able to see a significant temp difference among them ? If you are GOOD and do not have the excess vibration, then all 3 cylinder head areas will read about the same. If the BAD vibe continues I suspect that one cylinder would still be cooler than than the other two.
I'm thinking this test may at least give you something factual/measurable to point to, proving there is a problem.
Armed with this data, you should be able to get the dealer (OR an authorized by the dealer shop closer to you if that is that big a distance problem) to swap out an injector or flush out a line or whatever. IF THAT's THE PROBLEM...