2003 Ford Escape Sputtering / Rough Idol

My vehicle has been having a rough idol and sputters at times. It also had very litter power going up hills and mountains. I replaced spark plugs, fuel filter, fuel pump, EGR valve with no luck. I took it to the garage and after $568 they replaced the rear catalytic converter which was "clogged". They also replaced the spark plugs (again) and did a tune up. I picked the car up and it now has power and actually gets up the hills and mountains with no problem again. HOWEVER, it is still sputtering and almost feels like there is a "hiccup" or "air bubbles" when I am driving and begin to start up a very small hill continuing my same rate of speed. My vehicle also still has a rough idol as well. Also my check engine light was on prior to taking it to the garage and when I got it back the light was cleared. However it did come back on the morning after I picked it up from the garage. I know this sounds stupid, but I feel like the sputtering is worse when the weather is rainy or damp and this issue has been present for the pas few months. I'm not sure what else this could be and i'm hoping it wont cost much more money. I did call the garage last night and left a message with no response yet. I'm hoping you can provide some input to these issues.