Anyway, the fan does not seem to be kicking it, I will check the connector and switch shortly.
99% sure this is your problem. It should be coming on if you are saying the bike is overheating with the fan not running. As T-Cro said, jump the connector at the switch, and the fan should run. If it doesn't, it is either the fuse (stand alone - mounted just above the J-box with a white cover) or the switch (of course it could even be a chaffed wire).
The cooling fan switch is inexpensive if you go to an autoparts store and tell them you need one for a 1991 Honda Civic DX. The thermostat is from a 1983 Honda Accord (I'd recommend a 195 degree one, but stock is around 185? - your choice). A radiator cap can be obtained from a 1978 Ford Fiesta. This was all obtained from the parts conversion table. If you need the o-rings for the thermostat (and you will if you open it) order the kit from Murph for $12.50. I've used the switch and thermo on the list with no problems. Haven't needed the cap yet. Make sure the thermo has the little hole in it to burp, or drill a 1/16" one yourself.
O-rings -
http://www.murphskits.com/catalog/product_info.php?products_id=428