Shinlee, I've had the experience of doing this, basically a 90 A4LD into my 93, same as ur situation. Like Elusive said, it does not have the computer controlled lockup, that's where the lack of that third prong comes in on your 89 tranny. If I remember correctly that third wire just controls the torque converter lockup solenoid, and the other 2 are for the 3/4 shift and a ground I believe, which u do have on ur 89. I never got a CEL off of running just the two wires, but if u run a diagnostic test and get the codes out of the car, it'll throw some code about that solenoid malfunctioning.
You have two possibilities:
1)Hook up those 2 wires the 89 had, just use the connector from the 89 and splice the correct 2 wires to the 92's wires and terminate the 3rd. The side effect I got from that is a nasty jerk from the torque converter locking pretty harshly, usually when it's not supposed to. You'll really feel it, even just tapping the accelerator with your little toe around 45-55 mph. Doesn't cause any serious driving issues, it just gets really annoying pretty quick, lol.
2)Don't hook up the wires at all. I ended up doing this after awhile because the jerking got pretty bad. This will run the car in closed loop so that it doesn't lock the torque converter. I read through the ford factory cd and what happens when you do this is that 3/4 shift solenoid goes into "Failed On" mode, and the side effect from that is that u'll get a little less acceleration from a stop (it is noticable, but if ur lookin to bark some tires, an A4LD isn't the way to go anyway, lol). Why this is, I'm not entirely sure, I thought for the longest time that the converter was just crap and slipping when I hit the gas, but this actually is a known issue w/Ford. This will also get you a little less efficient gas mileage in mid cruising speeds, as the whole lockup idea was intended to help that. Not a serious amount, but less than you'd be getting otherwise.
I got a little tired of both ways, and it'll make u REALLY think abt just swapping to a t-5, but it will definately run the car, and it will shift through all the gears. Hope this helps!
I completely forgot about the lock up converter. I've slept a pretty long time before I had to think about this stuff.
