I've just realized that the stumble isn't REALLY that much noticable, but it is there.
. . . the whole transmission/drive seems to be a bit noisy / causing minor vibrations - how much is normal with these bikes?
The stumble is not there for me and neither is the rattle but I expect my motorcycle to be noisier than a Prius and maybe don't notice what others would. How much vibration is normal is impossible for me to say. Some people are more sensitive to that than others. The bike should not vibrate so much it blurs your vision, I guess. or knocks off your helmet.
It is an old bike with a lot of mileage. Air leaks can be at crankcase ventilation, at throttle body manifolds and at the air box. Read
this link. Visit the
Technical Library Card Catalog for more information. All hoses might need to be replaced with the correct type. Is the air filter clean? The fuel filter should be replaced; the tank should be checked for debris and cleaned if necessary. Are the injectors working well? Are the spark plugs in good condition? How do the spark plug wires look? Do they light up in the dark? :nono :giggles
Do all that, set the valve clearances then balance the throttle bodies. Read
this document. It illustrates and explains most of the systems.
Take off the final drive and lube the final drive splines, lube the transmission output splines, remove the transmission then lube the transmission input splines.
Nothing to it!
Otherwise, just put clean fuel in it and ride it until it stops. :hehehe