| My 95 916 SP has just succumbed to the rectifier/regulator/wiring problem suffered by many.
The first symptoms I experienced were a slight splutter and misfire on a neutral throttle in the middle of the rev range, which got worse as the day progressed, until later on in the day when it got really bad all through the rev range....and the bike couldn't be ridden (and yes, it was fitted with a new version reg/rec).
Now this doen't sound exactly like your problem (which does sound TPS/ignition/chip/vibration related...but perhaps whilst your tinkering, it may be worth just checking your wiring leading to the regulator/rectifier?
For peace of mind if nothing else! | 
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