engine surging & car bucking

Please stay with me here, as this will get lengthy.

There is a small electrical motor on your engine's throttle body called the "Idle Air Control". This motor extends a tapered rod, or pintle, into a tapered hole in the throttle body to control the amount of air the engine is fed during idle. The IAC motor is constantly active during idle, receiving commands from the engine's computer. The computer is programmed to send varying voltages to the IAC to get the idle results that it expects based on some constants. One of these constants is the diameter of the hole and pintle. But during normal extended use (as would have occurred by now on a '94 model), varnish and crankcase gases delivered by the PCV system will cause a buildup in the air passage and on the pintle which in effect changes their diameter. This change in diameter changes the amount of air that is allowed to bypass as a result of predetermined computer commands. Anticipating this, the engineers gave your computer the ability to "learn" exactly what voltage to apply to the IAC to get desired idle results, given the changing amount of crap that has built up in your throttle body during normal use. The snafu occurs when the battery is disconnected, as would normally happen when a TRANSMISSION IS REMOVED. When the computer loses battery voltage, its ability to "remember" what it has "learned" about how to idle this engine, with exactly this state of buildup in this throttle body, has been "forgotten". When the battery is reconnected, the computer will now assume that it is controlling an IAC with a CLEAN pintle in a CLEAN throttle body. If that is not the case (which it isn't) then the computer gets "confused" when it doesn't get the desired results from its commands, and will do some real funny things in its attempts to control the idle. What has to be done is to "relearn" the computer:

You will need a can of aerosol intake cleaner, available at any auto parts store, and an old toothbrush. Make sure the engine is COLD before you begin. NO smoking or other hot surfaces in the area. Disconnect the negative cable end from the battery (if there is any battery corrosion, now is the time to clean it up with a battery terminal brush that you can get at WalMart for about a buck fifty). Remove the flexible air intake from the throttle body. Open the throttle and pack a clean rag about 2 or 3 inches past the round throttle plate. Spray all in there that you can see up to the rag, and scrub it with the toothbrush. Then spray again until any solids that you have loosened are rinsed out. You may want to have a can or a small pile of rags positioned under the throttle body to catch the mess that is going to run out. When clean, remove the rag that you packed in and reassemble the flexible intake to the throttle body, and reconnect the battery.

Make sure all of the mess has been wiped up, evaporated, or sprayed away with the garden hose, as that aerosole intake cleaner is flammable. Now start the engine. It may not want to run very well at first, so you may have to help it by feathering the throttle pedal some, but don't overrev the engine. Let it get to normal operating temperature while holding the throttle to around 1500 - 2000 rpm's. Then, with no more throttle than is necessary to just keep the engine running, and NO throttle as soon as is possible, let the engine idle on its own, shifter in Park, for about 5 minutes. Then apply the parking and foot brakes and put the shifter in Drive. Only help with the throttle as necessary. When the engine seems to be able to handle this, while still in Drive turn on the AC. When it can handle that load, and leaving the AC on, turn on as many electrical devices as possible (headlights, wipers, radio, etc). All while you are going through this, the computer is relearning how much voltage to apply to the IAC to get desired idle results, and some patience may be required. You may have to sit there for 20 minutes or so while it is learning. After it seems to be able to handle things, shut the engine off and let it cool down. When you next start the engine, the computer will have relearned how to handle the idle IF there has been no component failure or any wiring damaged during the transmission removal/replacement.

I suspect that the engine is running roughly during this time and the problem is check-engine-light related. A 4-cylinder engine that is running roughly will make for a rough ride, especially in an Escort.

What could be making the engine run roughly only occasionally and only between 55 and 65 mph? It seems strange to me that the ride smooths out by going 70. This first happened after 9 hours of driving. I took it to a Ford dealer who diagnosed and replaced a malfunctioning air regulator. My gas mileage improved, but the problem recurred after a week. Can anyone be more specific about what the problem might be?

I'm sorry if I offended you by asking for something a bit more detailed. It has just been rather difficult getting anyone to give me any ideas as to what the problem could be. You never know who might have run across a similar problem. And there are certainly people such as yourself who know oodles more about cars than I do. I drive it, know when it's time for an oil change, and pay attention to any changes, but that's the extent of my car knowledge/ability. As my usual mechanic told me that such an intermittent problem could only be diagnosed when it was actually happening, it seems I am in for lots of potentially wasted money on extensive diagnostics or unnecessary repairs. I was just looking for any possible advice that might help reduce that load. Again, I apologize.