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Discussion Starter #1 (Edited)
I finally got around to writing this how-to up since doing the swap on my 1988 MX-6 GT. There are many parts that have to be changed and this is not an easy project. The only reason I did mine is because my automatic was toast and I did not want to spend the money to rebuild the auto. The rebuild on the auto trans cost more than the car was worth IMO. The easiest way to get all the parts is to find a parts car that is complete. You could strip the parts from a car in the junkyard but it will take a lot of time. Keep in mind that there were two different series of the first gen cars (1988-1989, Series A/1990 -1992, Series B). There are some differences so make sure the donor car is the same series.

I did some extra work to the car when doing the swap as the car was intended to be for my mom. I pulled the engine and thoroughly cleaned the engine bay. Every hose, belt, and seal on the engine got replaced while the engine was out. It is not necessary to pull the engine to do the swap, but I wanted everything clean and new. Before I got the car done, I found her a nicer car. So I got to keep the car.

I might add that I am writing this up months after finishing the swap and I have very few photos. If I miss something let me know and I will add it in.

Here is a list of parts you will need:
All four motor mounts and bolts/nuts
Flywheel, clutch, pressure plate, throwout bearing, and pilot bearing
Slave cylinder, hydraulic line, clutch master cylinder
A good transmission (the first one I installed was bad)
The correct bolts to mount trans to engine
Manual trans axles, connector shaft
The front strut mounts and spring seats are different, but they don't have to be changed
Shifter assembly
Pedal assembly
Instrument cluster (to get the blockout plates for gear indicators)
Wire harness (the one that runs along radiator support, LF fender, and into fuse box on driver‘s kick panel)
Wire harness (alternator harness, goes from alternator to fuseable link box under hood)
Alternator from 5 speed car
Exhaust from down pipe to Catalytic converter, and all mounting hardware (I used the auto flex pipe and ran new piping back)
The auto/ manual transmission throttle bodies are different, I have not changed mine and it works fine

Like I said, the list of parts is fairly long. Some parts don’t have to be changed. You can use the auto harness if you like and change around some of the wiring to make it work. I won’t go into that as I don’t know what wires have to be changed. I had a parts car so I wanted to make my car exactly like it would have been if it had been built with a five speed originally.

Here is a list of the tools you will need:
A couple of floor jacks and two pairs of jack stands, at a minimum
An engine hoist is helpful if you have one
A torque wrench
32 MM Socket and breaker bar (for the axle nuts)
Plenty of sockets, extensions, and wrenches
A repair manual. A Haynes will do OK as it has torque values.
 
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Discussion Starter #2
Getting down to business

If you are stripping a donor car like I did, its best to park the cars side by side to make swapping parts easier. I won't go into the specifics of each step as those things are covered better by a repair manual. I will just briefly cover each step that I went through for my conversion. It is not necessary to pull the engine even though I did to clean up the engine compartment.

Also remember, always think and work safely. I won't be responsible if you do something stupid and injure yourself.

On the auto car:
-Start by removing the hood
-Next remove the battery
-Jack up the front of the car and put it on jack stands
-Remove the front wheels
-Drain the radiator, engine, and transmission
-Remove the battery mount and air cleaner assembly
-Remove intercooler pipes and hoses (if a GT)
-Remove the radiator and hoses
-Remove the grill, side marker lights, and headlights of the car getting the transmission
-Remove the bumper cover and reinforcement (to get access to trans cooler)
-Remove trans cooler and lines
-Disconnect fuel lines and wire harness from engine (lay engine harness on windshield)
-Unbolt the sensors on the firewall and secure them to the engine (easier than remembering where all the hoses go)
-Unbolt A/C compressor and lay it on radiator support (leave hoses connected unless your a/c system is empty)
-Remove splash guards on both sides of wheel wells
-Remove axle nuts
-Unbolt brake calipers and secure them so the hoses are not holding them up
-Unbolt hubs from struts and lower control arms
-Remove both axles
-Remove exhaust from exhaust manifold to catalytic converter
-Disconnect shifter mechanisms (on the top of the auto trans, linkage and brace on the bottom of manual trans)
-Disconnect transmission wire harness
-Remove intake manifold support and axle connecting shaft
-Remove auto trans inspection plate and unbolt the torque converter to flex plate bolts
-remove the starter
-Break the transmission bolts loose but don't remove them

Now that everything should be out of the way you can unbolt the engine mounts and pull the engine and trans out together. Many of these steps can be skipped if you are only removing the transmission. Removal of the engine/trans from the donor car is very similar to the auto car.

With the engine and transmission out you can separate the engine and trans. The torque converter will puke some fluid out when you separate the two so be prepared. Separating the manual trans should be easier and less messy than the auto.

-Remove the flex plate from the auto car and the clutch and flywheel assembly from the donor.
 

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Discussion Starter #3
While everything is apart it is a good idea to clean everything up. I would recommend replacing all the rubber parts too, such as rear main seal, cam, crank seal, and hoses. You could also replace the water pump and timing belt. Replacing these parts now is much easier than trying to replace them while the engine is in the car.

Back to the fun:
-Remove the steering column from both cars
-Remove clutch master cylinder from donor and remove pedal assemblies
-Remove center consoles from both cars
-Remove shifter assemblies from both cars
-Install manual trans shifter assembly

Swapping wire harnesses: You will need to swap the wire harness that runs along the radiator support, under the front fender, and into the interior. Unfortunately, the harness also runs behind the dash and heater core, so they will have to be pulled too. There is a write up on how to pull the dash in the FAQ's that I found quite helpful.

Once you have swapped the harnesses out you can reinstall the dash and the pedal assemblies. Before reinstalling the gauge cluster swap the gauges to eliminate the gear indicators.

-Reinstall the center console
-Install flywheel and clutch assembly
-Reassemble engine and transmission
-Drop engine and transmission into car

The rest of the assembly is the reverse of the removal. You will need to use the manual trans axles, connector shaft, hubs, exhaust, and other misc parts from the donor car.

I am sure I have forgotten some things since doing the swap, so if I have missed something let me know and I will add it in.
 

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Just send a PM over to Panther and he will get it into the F&Q's
 
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