I've had my bike for about a month now and have put over 1,000 miles on the odometer so far. Recently the engine light has been coming on, but it only stays on for a few seconds then goes out, but it comes and goes several times within an hour. It seems like the engine light only comes on towards the top-end of 2nd and 3rd gear after I've been riding for an hour, then goes away a few seconds after I've switched to a higher gear. To me it seems like it may be the engine overheating. What do you guys think?
I doubt it's indicating that it's overheating, you need to check the codes, one should register every time the light comes on.
Based on you description I would guess you'll get a "voltage high" or "crank position sensor" code.