the most common reason for the gear shift being rough is either low fluid or a build up of varnish on the shift valves.
the usual fix is to have the transmission flushed out and the fluid replaced. It will run about $130 to do this. flushing will get all of the fluid out as opposed to a drain and refill and it will dissolve the goo that hangs the shift valves up. they can tell when the fluid is removed if there are any signs of internal problems. an inspection will show if there are any external leaks.
its the first step. chances are its just an accumulation of varnish on the shift valves. Make certain they only use the Hondamatic fluid to refill the transmission; otherwise you'll have problems with seal leaks and possibly damage the internals if you use Dextron. Dextron should only be used in an emergency.
hope that helps
