Not sure if this helps, but I had a similar problem with an NSR. Would run fonr for about 15 - 20 mins then run rough, then one cylinder, then die completely. Parked it up let it cool down and then it was off again for another 15 mins. Turned out to be the CDI, so maybe have a look at that as well. Should be easy to swap parts from someone elses bike in until it stops doing it.
If they're faster than you make sure you then give them your old parts back.
Hilleye
If it doesn't bring a tear to your eye, add a little more fully synth 2T to the mix.
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