After riding my bike for about a half hour to 45 mins, it gets hot. But it only acts up at stop signs or stop lights, like it wants to cut off, but I keep it going by using the throttle. It will start right back up however. I have water circulation, which tells me the water pump and thermostat is operating like it should. I put the fan on a toggle switch, and it still does that even with the fan continuing to run. I've burped the system to where there are no more air bubbles coming up. Anyone have any clue? I need help with this, I have to get this bike ready for our 2015 Riding Season.

 

Is your reservoir bubbling after the bike comes up to temp?

 

A lot of people notice that and experience same symptoms. What happens is the ignition doesn't get enough power, somehow the fan "steals" it. I've worked in cars for a long time and some years ago and was used to see the cooling fan cicle and the gauge needle drop a few milimeters but that doesn't happen in bikes. Things to check: Does it cuts out with a freshly charged battery?
Did you visually check your thermostat?-It can go bad without warning, permanently closed/opened-
Spark plugs - How long and how they look like- spark plug connectors are clean inside or dirty?
If the spark plugs indicate "rich" mixture do check:
air filter, and spark plug connectors for bad contact;
intake and exhaust for carbon build up you can see it by removing intake and exhaust headers.
This last one will slighty overheat the engine and will not let it cool down, carbon is like a sponge soaks up gas and heat(leading spark plugs to look dark) . This kind of overheat may not be noticed because water coolant sensor only measures coolant not metal temperature.
Finally the weather, do check for bad connections and be generous when using dihelectric grease.
P.S. Sorry if I misspelled anything.

 

Something else to consider, I had the same issues as you and I was scratching my head, eventually I replaced my R/R and it solved the issue. Sadly I lived with it until my R/R went out which found my solution.

 

No, the water does not bubble, I have great circulation, and I've burped the system many many times. No more air is coming out.

 

What's the R/R?

 

All the info you provided seems promising. I am going to change the spark plugs this weekend, because I know they had to be changed last year and did not do it. I will let you know the out come!

 

Does the flow ever stop? Too much flow from a stuck open tstat is not good.
How hot does it get? They always heat up more when not moving or in traffic. 50 degree increase is normal, with 230 at the top.

 

The more I think about it, it doesn't have the signs of getting hot. I assumed it did by the way it was acting, but never did it boil over or anything. I think the posts about it needing spark plugs and/or air filter, might be the problem. I was going to change the spark plugs last winter, but got to lazy. I pulled the plugs and air filter today, well lets say, I'm pretty embarrassed. I took some pictures, you can view them here!

 

The air filter doesn't look too bad... but those spark plugs look nasty. Check the coils for corrosion on the spark conector, clean and lube with a little of dihelectrical grease corrosion tends to ruin the pin that holds the spark plug.