For a month or so my '02 has had a strange symptom: vibration when riding had become variable. For instance -- on my way to a used tooling dealer there were practically no vibes through the bars or pegs, but coming back it was a bit more than what I consider normal. Checked all the usual suspects and nothing was loose. Fast forward to a week ago and another symptom showed up: the shifter would move slightly whenever I got spirited with the throttle. This I was familiar with from racing an old (~73 I think) Kawasaki Z1 that would do that whenever it was on the track due to a very flexible frame. Bracing it took care of that problem but created several others. Needless to say I stopped trying to make a silk purse out of a sow's ear and retired it.
Bracing the 919 frame wasn't an option, but I did find the problem: the lower rear engine mount bolt had not only come loose (first symptom) it eventually fell out (second symptom)! Since I was unwilling to park it until I could obtain a replacement 10mm - 1.25 X 200mm grade 10.9 bolt I scared up a piece of 7/16ths oil hardening rod stock, chucked it up in the lathe at work, turned it down to 10mm minus a tad, single pointed threads on both ends, and once I was sure it would fit used a rosebud to heat it to straw colored and quench it in oil. It's now about 3/4 hard, or close to 10.9 grade. With the 2 high grade steelock nuts I got out of bench stock I was ready to secure things properly.
This was not as easy as I had hoped. On the center stand the holes in the lower frame mounts were about 2.5mm out of alignment with the engine mount, and no amount of jacking the frame or engine would bring them anywhere near alignment. The problem was cured when I took it off the center stand and used the side stand instead. It aligned perfectly! Kind of weird, but at least it did line up.
All that was left to do was loosen all the engine mount bolts (with the new lower rear bolt in place) and sequentially tighten everything down. Problems cured, and the shifting is a bit more positive. The end result is most of the vibration in the bars and tank is now pretty much gone, yes even in the most common 5,000 to 5,800 rpm range, but a bit of a downside is there is now more vibration in the pegs. I can live with it.
Needless to say I have added checking the tightness of the engine mount bolts to my usual oil change checklist.
Your alignment issue regarding center stand vs. side stand reminds me of a post about GIVI crash bars and how the fasteners could only be aligned while the bike was on the side stand.
Yep, it happened to me, I tried to install a set of Givi crash bars while on the centerstand and the front mounting holes were off by 1/8" to 3/16". Before the next ride, I'll be checking all of the engine mounting bolts...
What is most impressive is you are astute enough to register those variations and know to be on the lookout for something out of place. The vast majority of riders would never even notice the change in vibrations.
You can actually jet carbs using the same method. The engine will have a harmonic balance when the carbs are jetted properly that you can feel through the chassis if you are paying enough attention.