Protege Misfires randomly
 

Hi, I have a 2002 protege se, 1.6l, automatic. I had trouble last winter with battery and it was difficult to start the car, which ended up causing Misfires at idle. The car Misfires randomly ( sometimes it would not misfire for a while). If I put it in neutral at red lights it reduces. If I throttle harder, then the misfire increases and the check engine light flashes. I replaced the spark plugs, the misfire was gone for a couple of days, then it started again. I replaced the battery and noticed a difference for a day, even though it didn't make any sense to me, I was relieved it solved the problem. But, she started misfiring again. I tried cleaning MAF sensor, changed air filter which was dirty, but none resulted positively. When I tried driving with the MAF sensor disconnected, everything was fine, battery light was on and the car shut off when I stopped.
Does anyone know if it is a bad MAF sensor. Help me end the misery of driving a car that sounds like a chopper motorcycle at red lights.

did you check for vacuum leaks?