2003 Ford Explorer Missfire and hesitation

Ok this thing has thrown me for a loop and I think I have it figured out however I want a second oppinion. My 2003 ford explorer is the 4.0 flex fuel version with a horrible rough idle and hesitation, misfire while driving at all speeds. It has only had the check engine light come on once and it was a cylinder 3 misfire. It seems worse when you are maintaining a steady speed where the engine is kinda just coasting and keeping up not under a severe load. I tuned it up plugs, wires, coil, fuel filter and tps. Still doing the same thing, it was better for a bit and then went back to the same old way it was running, like crap! I also changed the air filter and nothing helped. I recently took the air filter out totally and have driven the car several miles without it in and the car runs a hundred times better, no hesitation or misfire if there is its minimal. It however does still have a rough idle but not near as bad as it was. My answer to this problem seems to possibly be the mass air flow sensor but I want a second oppionion. Any thoughts? Thanks for your help.