Hi
Did you use pattern gaskets for the top end of the engine. If you did theres a chance that the big waterway hole in the base or head gasket is not punched out properly or not there at all! This happened to me with my first dtr and give the same problem you are having, if this is the problem it will overheat very quickly and the main collant hose will expand a fair bit also.
Take your thermostat out from the small housing in the head and drop it in boiling water. It should open up quickly about 6mm. If it isn't leave it out of the bike and replace the housing and gasket. re-fill system with water and run bike . If it doesn't overheat then its your thermostat, but generally these give years of service. If its pattern gaskets you used then I would definately suspect this as the cause, especially if the bike didn't overheat before the rebuild. Yamaha base and head gaskets are about £15 for both and should always be used as they work. Definately take the other guys advice as to skimming the head flat, but you will soon know if this is the problem as they usually piss water everywhere or leak water into the combustion chamber giving extremely rough running and reluctance to rev. Hope this helps
nick, May 2008