Hey so I've noticed this twice in the past month or so. If my bike gets low on fuel (start of reserve or so) my bike begins to run bad.

I would describe it's running very similar to a dirtbike. It's got that throaty sound and constantly backfires. And it doesn't really rev above 6K.

The bike usually isn't warm when this happens either. If the bike warms up then it goes away so it makes me wonder if it is a fuel issue?

I am at school and so my bike is kinda exposed to the elements and I wonder if water from rain is getting in the fuel? or even getting in the muffler and essentially clogging the system??

I think it's fuel because of the backfiring but could it be the engine because of the fact that it goes away when the bike warms up.

 

Well first any motor shouldnt be reved up too high until the oil is warm or you'll have excessive engine wear.

Other than that I'm not sure what kind of fuel problem would only happen when its cold, like a FPR, injectors, fuel pump...

 

I agree. Similar things can happen in a car and it usually turns out to be the injectors or fuel pump.

Best of luck.