Like he said, take it back. I've got a great Tech and the one thing he told me after he reprogrammed the ECM was that sometimes it doesn't take so if the truck didn't seem right to bring it back in.
As for the check engine/Mil light this link will tell you how to pull the code.
http://cumminsownerz.com/f13/how-get...r-dodge-ram-3/ and please let us know what you find out because we're all in this together.