You had your battery disconnected didnt you?
Since you had your battery disconnected, your ECM needs to re-learn the idle. I had that problem with my car when I installed my custom stereo.
http://www.automotiveforums.com/vbul...05#post2728605
that is the link to my post, there was a guy on there that told me how to re-learn the idle. Its in his post on there. near the last post. Try it, and make sure when you do it, That all the extra electronics are off. IE: Radio, lights, that kind of thing.
but this should take care of the rough idle.