Good Day,
I have a very similar problem on an 03 twinspark GS, that has been driving me batsh!t for about two years , so much so that it is about to get traded in or set on fire.
The bike will run fine until about 4500-5000 (70 - 80), when it will start to splutter and misfire (run fluffy sums it up) sometimes it will run through to 120, but still rough (not tested on public roads) . I have changed the stick coils, the ECU, the lambda sensor (after a visit to Steptoe showed it to be faulty), swapped out the injectors, changed the airbox sensor. The TPS is set spot on at idle according to Steptoe's diagnotic tool.
The bike seemed slow to crank and initially would not crank until I removed and cleaned the starter. Next component to change is a second hand TPS, in case the TPS is out at higher revs.
Does anyone have any other ideas? I also have an ECU if anyone needs one.
You mentioned disconnecting the QR, which one did you disconnect.
Did changing the fuel regulator work?
Cheers