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I have a fuel injected 2011 250R. I haven't had it stall, but I have had the FI light come on and the temp gauge max out. In my case the problem has always seemed to stem back the electrical wiring (the "loom" I think it's called). What seems to happen is that some parts of the loom get water in them and cause corrosion. This has affected the behaviour of my throttle at times and during cold weather has seemed to have made it difficult to start the bike. The problem was fixed for me recently when a mechanic chopped off and replaced the corroded wiring with new wiring.
I think a mechanic can easily test for corrosion by:
1) visually inspecting the loom.
2) using a multimeter to test for resistance on the wires.
I don't know if you will have the same problem as me. I'm not a mechanic. I know very little about bikes. It's possible we've had a similar issue though.
One more thing: a Kawasaki dealer should be able to hook-up a proprietary Kawasaki device to the FI system chip to get a read-out of what the last error was. That may also help to diagnose the problem.
Note: I also have a Power Commander on my bike (PC-V). The PC-V hasn't caused me any issues.
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