Comments are BELOW the pictures.
Wiring convention: If the wire is stated as a single color, that is the only color of the wire. If the wire is stated as two colors (ie - YEL/BLK), the first color is the primary color of the wire and the second color is the color of the stripe.
Remove hood. Do not disconnect the battery yet!!!!
Remove the center console cover to expose the shifter. Two phillips head screws on the sides hold the shifter handle in place - remove the shifter handle. Four phillips head screws (you can see them here...they're gold) hold the shifter faceplate in place - remove them and the shifter face plate.
There are three plugs that need to be unplugged - a 10-pin plug, a 2-pin plug (large gauge wires), and another 2-pin plug (small gauge wires).
As oriented in the photo above on the 10-pin plug, remove the two wires on the top row (closest to the clip) all the way to the right (as viewed above from NON-wire side). The wire colors are BLK and GRN/WHT
Solder these two wires together. This will make your car think it is in park all the time. To verify that you have connected the correct wires (this is also how I figured out which ones to connect), turn the key in your car to the on position (2). The gauge cluster should show that the car is in park (P will be lit), even with the plugs disconnected from the shifter. Turn the car off and put tape/heat-shrink over your solder job.
I had already put a 5-speed cluster in my car, so I took this part out of my old auto cluster and plugged it in. You can see that the P would be lit on the cluster, regardless of what position the shifter is in.
Back at the shifter, cut the plug off the 2-pin plug with large gauge wires (BLK/WHT). Solder these two wires together and put some heat shrink over the connection. This will allow the starter to get the 12V it needs to start the car. Once you've done this, you can go ahead and start pulling the engine and tranny.
Dad gets to work removing the axles (be sure to drain the tranny fluid before you pull the axles)...
...while I get to work disconnecting the automatic shifter cable from the transmission. To disconnect, put the shifter in the neutral (N) position. Get under the car and remove the sheet metal access plate (sometimes called the flywheel plate) to expose the torque converter. Once you can see in there, you'll need needle nose pliers (and lots of patience) to pull out a cotter pin. Once the cotter pin is off, a small metal clip comes out and the cable comes off. Don't forget the 12 mm bolt at the rear of the tranny that holds the cable sleeve on.
Unbolt and remove the auto shifter. There are bolts in the cabin and under the car that must be removed.
Drain all fluids - engine oil, automatic transmission fluid, and coolant. Be sure to do this before you pull the axles, or you'll have a mess on your hands.
Pull the radiator for clearance to get the motor out. Be sure to disconnect all electrical connections and all coolant and automatic transmission fluid connections before you start yanking. It's tough, but it will come out. Also unbolt the AC compressor from the engine (four 12 mm bolts) and zip-tie it out of the way.
Pull the motor. This is the proper angle when pulling from the top. I like to start with the engine balancer all the way to the left and chain it up where that is level. Then loosen all the mounts and crank the balancer all the way to the right...this gives the best angle for me every time. I went ahead and removed my front crossmember just for added clearance when pulling the motor. If you want to pull it, remove the front engine mount bolt, four bolts holding it to the frame, and four bolts holding it to the front lower control arms.
This is the rear engine mount. This is the whole reason why I pulled the motor too. The mount must come off. Three 12 mm bolts hold it on - one in front, two in back. I used 3/8" drive ratchet with 6" extension, universal joint, then a short well 12 mm socket to get the back bolts off. No sweat.
Another shot of my setup to get the back bolt off. You do NOT have to drop the rear cross member to remove the auto mount.
LEFT - manual transmission rear mount and bracket. RIGHT - auto transmission rear mount and bracket.
Rear mount removed. You can see there are four bolt holes, but only three bolts to hold the rear mount on. The back two holes are used for either the auto or manual mount. The front right bolt hole in this view is used for the auto mount. The front left bolt hole in this view is used for the manual mount. Be sure to use an appropriately sized tap to chase the threads in the front left hole before you put a bolt in - it's been exposed to the elements for over 20 years and could use some cleaning.
Install the manual mount. You MUST lower the rear cross member to do this. It's not as bad as it sounds, I promise. There are four bolts that hold the rear cross member to the car - two on each side. I unthreaded the bolts on the driver's side about halfway and completely removed the bolts on the passenger side. My dad put a little pressure on the cross member pushing it toward the front of the car, and I was able to slip my setup behind the mount and tighten the back bolts. After that I simply put the four bolts back in and tightened them up. The rear mount is IN.
Dad separates the auto tranny from the eingine. We spilled ATF everywhere - it started pouring out of the torque converter! Be ready to clean up a mess.
Remove the torque converter. It's a bunch of 10mm bolts. You have to loosen them from the area where the sheet metal access panel would go on the bottom of the engine. After that it pulls right off.
Unbolt the torque plate. It's six 17 mm 12-point bolts. I used an air impact wrench. These bolts are stamped "AT" for auto tranny. They will not work to bolt on a flywheel (too short). You need to get some flywheel bolts (stamped with "MT").
My rusty flywheel before resurfacing...
Freshly resurfaced flywheel. Be sure to take out the old pilot bearing before you take it to get resurfaced.
Use a seal/bearing driver to install the new pilot bearing that came with your clutch kit. It gets hammered in from the back side.
Pilot bearing installed. Make sure it is all the way in!
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