Motorcycle Repair: Will not start after running., water cause, air bubble

Question
I have a Honda CBR600F4i.  I know its not one of the bikes that you know but I highly appreciate it if you can help with this one thing.
I recently moved from San Diego to DC and the Navy shipped my bike. I had to drain the gas and coolant.  Once in DC I replaced the oil filter and filled the oil.  I also refilled the coolant.  First I had the problem of the fan not turning on around 220-230 F degrees.  Which caused the bike to over heat.  I learned  that I had to burp the coolant to get the fan to turn on at the right time.  During this time the bike turned on just fine when it was hot.  Now the fan turns on around 230 F degrees but the problem I am having is the bike will not turn bike on after running for awhile, while the bike is hot.  Once the bike is cooled off for a few hours the bike will start back up again.  I was wondering what would be the cause of this?  Did I burn something up when the bike was overheating? The oil seems to be filled correctly but can overfilling/under filling cause this?  Can the fact I did not use a motorcycle coolant or mixed it with water cause this? I don't want to waste your time but I am at a lost here.  I don't want to take it to a mechanic to be charged for something I can do.  Thank you for any help and/or guidance.

Jeremy

Answer
Sounds like you ran the bike with a fairly large air bubble in the system for a while.  No way of knowing if there is damage because of that over a computer line...  Use a coolant since it improves the wettability i.e. the cooling efficiency of the cooling system.  I believe your bike is a fuel injection bike, it may be that the computer just needs soem time to adjust itself to the different settings.  Run it for a while and see if the problem goes away, meanwhile check the plugs and check the way the engine is performing.  Good luck,  Jan