Fuel, Compression, Spark - in the correct order at the correct time.
Fuel - most likely culprit. If possible check the pressure at the fuel rail. I don't have the numbers in front of me, but it should be in the 30s? I have a jeep that does this occasionally, the pressure will drop from it's standard 35psi to about 5psi, and the engine will idle alright, but with an open throttle it stutters and dies. I've got a bad wire on the fuel pump that causes my troubles. Possibly a blocked filter or dirty/dead injectors. I actually pulled the fuel rail and injectors off of the intake and watched them squirt into the air once trying to diagnose a problem. I would NOT recommend trying this - nearly vaporized gas has a habit of exploding at the darnedest times. but I knew as I rushed for the fire extinguisher that the problem was not in the injectors
compression - you said that it was running on two...but timing won't really cause it to run on two - improperly adjusted timing will usually cause it to either not run, or to run really, really poorly on all four. Check the compression, especially on the two that you said weren't running before. you said it starts right up now - so it is doubtful that this is the problem.
Spark - 89 was still and EEC-IV system right? Usually when they go bad, they go all the way bad. Check that all the wires are good and have good connections (probably, but sometimes it is the little things
) check the vacuum lines especially the ones around the upper intake manifold...for that matter check and make sure that you don't have unmetered air coming in at the junction between the upper and lower intake sections. Last, take a flashlight or shoplight and look for any loose wires, again around the intake (both upper and lower sections - I can't go out and look now, but it seems like there is a sensor underneath the lower intake manifold) and around the airbox.
Everything else - recheck the timing, both ignition and cam timing. If the cam was put back a tooth off, it might cause symptoms that are similar to what you are describing - you night want to check the timing belt tensioner and make sure that it is holding the belt tight. I had one that the spring lost tension, and it allowed the belt to jum about 6 teeth. That was far enough to keep it from running at all.
I've also had a shear pin break on the distributor drive. the drive had enough friction with the broken pin and distributor shaft that it would turn the distributor when the motor was cranked, but when it caught, it would start slipping. (probably not - after the first time it slipped, the engine would not want to start)
Hope something here helps.
1989 mustang 2.3l lx hatchback need help!!! 
