Sounds to me as though something was retarding the timing. With the newer fuel injected bikes I would tihnk that the ignition rotor would not have a mechanical advance, but if it did, some condensate may have turned to rust and temporarily kept the engine timing back. It's also possible that the IAC valve got a little sticky from sitting and the computer kept pulling timing out to try to lower the idle. I find it very hard to believe that it would idle at all if it was lean enough to turn the pipe red hot.
That said always add Stabil to your fuel tank and ride it around a bit before storing for the winter to get the Stabil in the fuel lines and small orfices. Gas in small quantities goes bad much faster than in a 15 or 20 gallon tank. On something that's carbuerated, turn off the fuel tap and run the carb dry and keep the tank full. Keeping the tank full with Stabil in the fuel will keep rust from forming in the tank. Also, throw the battery on a trickle charger (1 amp) once a month.
Nice bike BTW! A buddy of mine is picking up a '12 KLR 650 this coming Tuesday.
