If you reset the ECU after the install ( and you should disconnect the neg. battery cable anyway when installing something like that, just to be safe) I'm pretty sure it's not an issue w/ the ECU adjusting.

Have you checked for vacuum leaks? Has the car been like this since you got it? If you got it like that, there's the possibility that the idle set screw was adjusted. From the factory it should have some epoxy or something over it, so you might be able to tell if it's been messed with.

Also, when you come to a stop (w/ engine warm) and it idles at 2,500rpm, does it go there as soon as you put the clutch in, or does it idle lower and then go up after you've come to a stop?