What does everyone think about the main cat? Granted it is an older model, well different all together, but I had a Miata brought in one time that had the same problems. Below 2000 the car ok, but get it above that and... well grandma would pass you while blowing her horn. Being young and since I did not have very much experience, my service manager let me battle it for about an hour. At that point he felt like I had done enough, plus I was at the parts counter getting prices together for plugs and wires.
Does the car sound muffled? Sort of like someone has put a pillow in your intake? If so, I would bet on it being the main cat. The main cat is not monitored, so it would not set a CEL IIRC.