1994 Toyota Corolla Car stalls at idle, jerks during drivin

I have a 1.8L 94 Corolla DX, and I recently had my rotor and distributor cap crack. I went to a mechanic and he said that 2 spark plugs were bad and i should replace all 4. He also said that I should replace the wires, the cap and the rotor. I went with all except the wires (which I replaced myself). He also did a tune up on the car and it ran great. I had an acceleration problem soon after where I had slow acceleration times which were dangerous during traffic for passing, accelerating from a stop sign onto 45+ mph traffic. So I replaced the fuel filer and Ignition coil. It seemed to fix the problem. Also replaced the upstream O2 sensor and cleaned the throttle body. Threw in some STP Gas treatment and Fuel injector Cleaner (different tanks of gas) just for kicks.

Enough with the background information. Now after all that has been fixed, I now have a problem whenever my car is at a stop light, or cruising. I thought it was a timing problem, but another mechanic said it wasn't just by listening to it. The car runs rougher after I changed the ignition coil and then it has the possibility of stalling. At higher cruising speeds (40 - 75 mph) sometimes it will jerk and the "Malfunction Light" will go on, then turn off after a few mins. If I leave the car in Neutral, the rough idle is gone and there isn't a possibility of stalling. If the car is in Park, it is also kind of rough with some jerks.

I read on other forums it could be anything from the fuel pump to idle control valve or something in the distributor. Can you please help me? I want to get this fixed before I sell my car.