Bike keeps cutting out!

the same symptoms in a car usually lead to a bad ignition module, gets hot and cuts out, cools off fires up, get hot cuts out....

So on this bike the ignition modules are all part of the plug wires, right?
 

Or is it the module in the rear of the bike?

should be a separate part. On my 95 its the larger black box behind the right side rear seat panel

pop a few viagra in the tank.  if the engine stays running for more than 4 hours, see a mechanic IMMEDIATELY.

how long do you ride before you notice a problem? is it just after warming up, or a little later? if you could be a little more descriptive, that would be helpful, because what you describe could be a lot of things.  really sounds like an ignition coil - just like mine on my f150 when it died in the rain ...but doesn't the bike have 4 coils?

It is usually about 5-10 minutes into my ride, just about when the engine is reaching it's normal riding temp. Im gonna try getting the new module and if that doesn't work i will replace the plug wires, which have the coils in them, but i dont think it is that because i think it would die completely and not correct itself after sitting for a little while.

might wanna chech the connect to the coil/wires as well.
http://www.ronayers.com/fiche/200_0371/wire_harness_99-00/wire_harness_99-00.cfm?man=ho&groupid=5230&parent=5220
 
you can see where the 4 plugs for the coils come into one plug. Check there, make sure there is no corrosion and such

I have step by step instructions on how to test my coils but how can i test my module? can i just use a voltage tester and how do i do it?

I had the same problem with my f2, the bike would run fine for about 5-7 min @ idle, then just die. It ended up that it was a combo of two problems.....
 
1. my vent into the fuel tank had gotten clogged with some sort of crap, causing the fuel to stop flowing.
 
2. the fuel line from the tank to the carb was extremely worn and was pinching off at the bend just before the split.
 
I spent alot of time figuring out the same symptoms you have  and thats what i came up with. a quick way to check is to run the bike until the problem occurs and the pull out the key, open the tank, close the tank and re-start the bike. if it starts and runs ok, your vent is most likely clogged. blow it out with some compressed air and you should be good to go. if thats not the case and your sure your getting fuel, check the ignition module. hope this helps!

I had the same problem and thats what it was.  I lifted the tank slightly and the vent tube had a little kink in it.  It would run for like 10 minutes and then cut out.