1998 Mazda 626 missing/making engine run rough

Electrical problem
1998 Mazda 626 4 cyl Front Wheel Drive Manual 120k miles

I just got my oil changed, spark plugs changed, air filter, Engine light has been comming on for 3 weeks, engine runs real rough, ac makes it worse. Feels like the engine is coming thru the hood, but only in 1 and 2 gears and than it takes off like a bat out of hell. I tried fuel injector cleaners, etc, my mechanic tried new plugs, changing fuel filter, he is stumped as welll.