Old topic I know but I was searching becasue now I had the same problem. This is just an insight on those who adjusted the TPS with no results, or don't have bad coils and still get these same issues. I solved mine but cleaning every wire connection under the seat the corresponds to the battery. I started by removing the grounds and positive terminals and wire brushing them. They were clean and didn't have corrosion but I did it anyways. There is a small box with two fuses next to the power cable that also has a white connector going into it with four wires, take that connector out and with a small file (what is used) or sandpaper clean all for of the spade terminals in the little black box and spray a contact cleaner in the white plug. I then moved to the negative side of the battery. Trace the negative cable back to the engine. You will need to lift your gas tank for this one, no biggie. There is a white single connector that ties to the negative terminal and connects to the main harness that runs along side the inside frame. Disconnect this and mine was corroded heavily. Clean this with file / or sandpaper really good!! This is what grounds your ECU (brain) of the bike. I think what happens is driving around it develops a bad ground and the ECU resets while driving but since the bike is in motion or in gear, it isn't quite dead until you pull the clutch in. I believe that this is why turning the key on and off temporarily fixes the problem... Now were was I, oh yea, cleaning the single connector, spray contact cleaner into the other side of the plug, there really isn't a easy way to clean this so this is what I did. Follow the larger black wire to the engine block and it should be attached by one bolt. With this bolt you can look on the top of it and see if there is any corrosion, if there isn't then dont remove, if there is remove it and clean it good. As a pre-cautionary measure I also ohmed the cable from tip to tip, if you ohm anything other than 0, there is corrosion in the cable and it should be replaced. Connect everything back up and also I pushed on all the connectors under the seat just to make sure they were all seated, even the ECU, then start! Its been running great ever since.
I'd like to add, I have a 2003 R6, I already did the TPS, cleaned old one, didn't work so bought new one. I did the valve adjustment, im at 24k. I have the carbtune and sync'd throttle bodies, it cleans up the idle, but it still died. Topped coolant, went through all the senors, cleaned air filter, changed oil, new spark plugs.
The above was the only thing that fixed this. I was never able to duplicate the problem in the driveway only when I drove. I stumbled across this becasue I had the bike running and the seat off and I started pulling and pushing on the harness and connectors, kinda hard, but not hard enough to break stuff, and instantly when I jiggled the main harness with the negative (white singe plug) my bike idled lumpy and died, Then I couldn't start the bike without the key on and off, so I cleaned everything. I was racking my head, hopefully this helps people who are at minds end like I was!!