Problems after Long Tube Install...

Last week I installed MAC Long Tubes and a Prochamber. The car has been running rough as I didn't have the 02 sensor extensions. The extensions arrived today and I'm still having the same problems. The car idles fun, but when in gear, it just dies unless I leave my foot on the gas. The check engine light won't go off either. Everything was properly reconnected. Any ideas as to what might be the problem?
Thanks,
Brian
 
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Oddly enough, my g/f (who is clueless about cars) happened to mention resetting the computer and I realized I hadn't done that yet, so I did it a little while ago. Car still occassionally dies when I come to a stop when in gear, not quite as often though. Check engine light is also still on. Will drive it around a bit tomorrow and see how she is.