Idling extremely rough, but normal driving down the road
 

Hi. I have an 03 SS with a non supercharged 3800. I was driving down the freeway a few days ago and it overheated bad. My temp gauge never went past the middle, though, so I didn't know it overheated until my engine shut off. Fastforward to now, I replaced the water pump, thermostat and did a power flush. No overheating problems now. My only issue is, while idling, it sounds like it's only firing on one or two cylinders. After the overheating incident, I figured it was because most of my water boiled onto my ICU and coils. This doesn't seem to be the case because I checked the coils by removing all of the
spark plug wires and having a buddy crank it while I watched all three coils spark correctly. I took it down to autozone and had them check codes. It fired P1131 and P1132, and then while I was drying off all of the components related to those codes, my check engine light went off (since my battery was unplugged) and now I can't get it to come back on after driving for 30 minutes. I also replaced the fuel pressure regulator. Any ideas?