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The main fuse is probably a short or maybe the regulator is a bit dodgy and fails when it starts to warm up. Possibly one of the diodes in it has gone bad, that could easily give you that kind of problem.
If this doesn't happen when you take the bars from lock to lock then the loom is probably OK and it is something that like above.
Alternator isn't likely to be the culprit, volts out do rise with revs (hence the regulator) but it shouldn't be a real issue. It ought to happen as soon as the revs rise.
Intermittent bad running.. plugs and injectors. Change the plugs maybe clean out the fuel system.
Both might be linked if the reg is dumping more random voltages, sometimes low but sometimes high enough to trip the fuse
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"The final measure of any rider's skill is the inverse ratio of his preferred Traveling Speed to the number of bad scars on his body." Song of the sausage creature
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