This is a pretty common problem here in Florida, but it's mostly the Northern blue-hairs not paying attention at the pump.VehiGAZ is on the right track with checking the exhaust, but there's more. I have a few local friends that are mechanics and they get this repair several times a year. Basically, they replace all fuel filters, check valves and spark plugs, inspect the vent lines, replace the catalytic converter and inspect the exhaust system. They also flush the tank and fuel lines as well. With a fresh tank of gas the engine usually clears right up.
Now, since this is clearly not your fault and there's ample evidence of where the error occurred... I'd go for whole new engine replacement using the 3.5 DI. Just to be sure. :winkg: