90% chance it is your coil packs. Chances are you have had one completely dead pack for quite some time and the other pack is failing on one of the coils. Had a very similiar situation with mine. Mine would be dead on a cylinder and then after 5-8 mins on the highway would come alive for the duration of the drive.
I went to a junk yard - robbed 2 coil packs off a mid 90's Ranger with the same motor setup, bolted them on and things ran normal. Got them for 20 bucks each with a 30 day warranty. Beats the 150 price for new at the autostore. You can always test individual coil packs by unplugging on of the connectors and attempt starting the car. If you unplug one and the engine doesn't fire - you know that the one plugged in is completely dead. plug the other one back in and unplug the other and see if it runs like you describe. If so, you have one dead pack and one in the process of dying.
the other two things it can be if it isn't this would be the DIS module (bolted to the front of the lower intake manifold - has a harness plugged in the top and bottom
or
the computer itself is starting to crap out.
Best thing to do is to unplug one coil pack and see if it runs the same or not at all. if you get no fire at all on one of the packs, then it's definitely your problem. If it runs the same when you try both packs individually, then it's either your DIS or computer.
