Chris wrote: Why wouldn't the 5 spd trans work? Didn't Toyota use the Z52 trans in both the FWD hatchback and the 2WD Wagon? Or was there enough difference in the trans tunnel area on the FWD wagon and 4WD that it wouldn't fit?
All of the floor stampings are different between the 4WD wagon and the 2WD wagon, every single one. The differences range from the extreme, such as the different spare tire location and lack of side "compartments" in the floor of the 4WD, to the simple, such as the 2WD not having the hole stamped for the insert to mount a dead pedal.
Mounting the 5 speed (or a 4 speed, or even an automatic) from a 2WD wagon or hatch would be possible, but it might involve more modification and fabrication that would be worthwhile unless a parts car was available.
At this point in the Tercel's lifespan, transmissions are becoming their Achilles heel. While there are still some available from the Japanese importers, they are becoming harder and harder to find. If a good used one is located, and you're planning on keeping your car, replacement of the bearings and syncros might be worthwhile to preserve your transmission and your sanity. Those transmissions were weak when they were new, and any preventative maintenance and care in driving will pay off big time in the long run.