The light never came on but the fans were going. It was just strange, I was riding then all a sudden it started to shift hard and then when going for 5th it was like I hit Neutral. Half way home I noticed my left leg and ankle was real hot like on fire. So when i got home i started looking around the bike and could feel some massive heat coming from near the footpeg/shifter area. The cover right there was so hot it melted my skin when I hit it with my knuckle reaching for my helmet. Is this normal?
Hard to tell from your description.
The left side front alternator cover by the shifter is going to get as hot as the engine oil is, that'd probably be upwards from 200 degreees F. If you're riding with your foot/leg touching that cover, it's going to get hot (can't tell if you're riding like that since I'm not there).
The fan coming on is normal. It would not be normal if it were on all the time, unless you spend most of your time sitting at idle and not moving.
Sometimes hard shifting can be caused by the clutch cable being out of adjustment (too slack).
If you're really concerned, you might check to be sure that the high temp warning light works OK. Then I'd only worry if the light keeps coming on.
YMMV, I'd check all this with the dealer/service who can actually check out the bike...