[aoncurly]

If you're getting pops (backfire), it sounds like a mixture related issue. A couple of things come to mind when I had some similar problems. For the backfire and rough running, I took my car to a mechanic and he did something with the air sensor plate. It literally took him like 5 minutes. He adjusted something, and said, "It sounds much better!" Sent me on my way and didn't even charge me.
More recently, I was getting some general rough running issues and my mechanic first adjusted the mixture, but after it still did not feel quite right. Took it back and he said he checked my plug cables by putting a towel over the engine compartment while the car was running. He said it looked like a Christmas tree with all the crossfire sparks in there. He replaced my plug cables, checked the mixture and the car ran much better.
Mixture problems are tricky and are related to so many things.
You said that your exhaust pipes were replaced. I hope the O2 sensor bung was properly welded or factory welded, as introduction to air in the exhaust is going to mess up the O2 sensor readings.