An often overlooked condition is an intake leak.
These can often cause inconsistent problems and conditions. The symptoms vary, hesitation, lean conditions, overheating and many others. An intake leak will not be limited to just the manifold seals. It could be worn throttle shafts, cracked or hard vacuum lines (i.e. V.O.E.S. hose), loose mounts and many others. The easiest way to check for leaks is the following. Fire up the motorcycle and hold it at a steady RPM (2000). Using an aerosol lubricant or cleaner (being careful of painted parts) spray all possible leak points one at a time. If the bike revs up or dies when an area is sprayed, it has a leak and needs repaired. If the condition persists double check your work. New gaskets can be damaged when installed.