I have a 2003 BMW R1150GS Adventure that I bought about a year ago to replace an aging and tired Honda V65 Sabre. So far I've been very disappointed in the BMW from a reliability point of view. Clutch slave cylinder blew out shortly after starting out on a modest 2000 mile trip, fortunately it was still under warranty at that time, and BMW fixed it.
Now, a much bigger problem: First appeared after crossing the Baja peninsula from the "cool" pacific side to the warmer (about 80 deg.) Sea of Cortez side in March. The bike just died, and would not start again. After waiting about 5 minutes, it started and ran fine. It did this a couple more times, and I started taking things apart: checking and reseating all electrical connections, pulling a plug to check for spark (OK), etc. Bike started after this, but only because it took some time to do all this. Now started riding it again in So. California, and it's hot 100+ deg. Bike would run for an hour or so, then die. It would take anywhere from a few minutes to hours of waiting before it runs again, and then sometimes for only a couple of minutes.
I am guessing that it is a thermally dependant problem with fuel injection electronics, but since it is an intermittent problem, you can't really test anything. Taking it to a dealer would probably result in me paying for all sorts of very expensive replacement parts on the off chance that maybe one of those was bad - and I still wouldn't know if the problem is fixed, until I wind up stuck in the middle of some desert... again.
Has anyone here ever had this kind of problem, or have any suggestions?

At this point, I don't want to use this bike for any long trips, as I have no confidence in the BMW, and think I made a HUGE mistake in buying one!