2001 Ford Expedition Running rough

I took my truck off the road for 3 months, It had 1/4 tank of gas in it. So when i put it back on the road and it ran like crap, I thought it was bad gas (water in it). So i drained the gas and added dry gas, Filled it up with 93 octane, But it still is very sluggish and runs rough. With the bad gas in it the check engine light came on. Now the light is still on. It ran perfect when i parked it so what could it be now? It has to be something minor right??