Originally Posted by
blindsquirrel
You'd have to track down a 2006 2.4L manual car, get the VIN from it, then SPS your existing ECM with that manual trans VIN (or buy one used pre-programmed to a supplied VIN). '06 2.4 is an E67 so you can't take the easy route of using a VIN from a 2.0 manual car (P12), which has tune files/VINs available all over the place.
However, there is a cheat... 2006 HHR 2.4L. VIN for one of those, same E67, built with a manual, is 3GNDA23P46S608485. Should not be any differences from the Cobalt engine hardware for a swap like you're doing.