tranny shifting problems

my 94 cougar has problems shifting between gears(auto) itll go to about 3500 or so stay there for a few seconds, about 5-6, then shift, idk if it has to do w/ the shift kit being installed or not but it really bothers me, according to the local dealership it needs replaced but im thinking it may just be in the computer, if u can give me some input it would be greatly appreciated!