OK, so you disconnected the battery cable from the terminal while you were installing the KKM, right? If so, it kinda depends on how long the cable was off to really make sure the ECU rest itself. If it was off more than 20 mins or so, it should be reset. You can really make sure it is reset by pulling the fuses in the engine compartment fuse box (there are 2 of them), or by taking the computer out and re-insatlling it (follow Chris Hightowers instructions
here.) Sounds like your computer is still re-learning the new stuff. You only ran it like 2 miles right? Let it idle for like 10 mins and see what happens...Don't drive it, just let it idle....