First I started this new thread, both us mods in your introductory thread didn't realize your problem as you posted after us, both of us and many more on this forum can easily sort this out, I have vast experience on the electrical side and am sure this is solvable without using the dealer , depending on how skilled you are.
The first thing is it sounds like you could possibly have a chain / sprocket problem as to the speed vibration. The shifter could be a combination of the pivot point being dry and improperly adjusted, that version didn't have a sealed grease area, also your engine oil could be a factor. As to clutch plates , in over 8 years on this forum, I don't recall one member with clutch plate problems, clutch cable yes, improperly adjust cable yes, pinched clutch cable yes , no lube on the clutch lever yes.
you mentioned the plugs, many have come across cracked stick coils, one option you could do to prove it is swap stcik coils, if the problem moves to the other cylinder you know you need new coils.
You mention about the headlight, you need to go over all your engine / frame grounds, I had several corroded grounds on my 07, as protection of electrical connections wasn't as good as the new 2015 Versys, that I have now.
If you have a good digital meter, you need to measure volts DC at idle 1350 RPM at the battery, you need to raise idle to 2000 RPM using the idle screw adjustment and measure it again. You then need to stop the engine and disconnect the plug from the stator and measure volts AC http://www.kawasakiversys.com/forums...gs-2015-a.html
TPS there is a harness made that is used for both the main throttle and sub-throttle, there have been members with TPS failure on this forum, there have been solutions to partial replacement, before considering this it is best to get these measurements, main and sub-throttle, FYI the full service manual is available in PDF from this site, look in sticky how to
You were very close,as to spark plugs, I would consider doing a valve shim check, ( there is a full step by step for every 650 made in the How To forum, including inline photos , as you said the dealer said vacuum sync was good, usually vacuum sync being off is directly related to valve shim clearance, so this is something I would consider but highly unlikely a cause of any of your problems.
You asked about photos