Same situation.. I can almost guarantee that the gasket between the intake manifold and reed valve block will be damaged when you pull it off. This happened on all three of my motors. My guess is the gasket had a factory adhesive on it or the combination of heat, pressure and time glues it to the metal parts.
Just reassemble with a coating of non-hardening Permatex 2.. the gasket, even if torn, will be effectively sealed.. (i'm speaking from experience)
Under the reed block there is no gasket. the rubbery reed petal sealer / block coating acts like a gasket and the part should pop off cleanly. (be careful you dont scratch through it with a prybar or something.. you don't want to rip that rubber coating.)
Before you take off the carb, spray some Starter Fluid around that area and listen for an RPM increase. If so you have a vacuum leak. I had one and after a lot of wasted effort tracking down a rough idle and misfiring problem, I finally found this leak. After that was sealed the damn bike ran great.
Otherwise, give everything else a tuneup before dropping the engine to remove the carb. If you can get it to run smooth all the way up to 30 MPH top speed you have pretty much reached the limit of the stock bike.