For this you will need to remove the axles, transmission, clutch, flywheel, transmission mount, front and rear engine mounts and brackets. The Dowel pin will need to be removed from the crankshaft as well.
As mentioned before you need to have the manual transmission out of the car and it tore down to the crankshaft. You will also need to remove the dowel pin in the crankshaft.
First its best to go ahead and change out the front and rear engine mounts and brackets to the automatic ones.
You will then put the crank pilot bushing into the end of the crankshaft.
Now is a great time to shave the wings on the rear main seal. I do not believe this is needed with a stock flexplate. It is REQUIRED for a Kiggle Flexplate.
Then you can put the flexplate on. If you are using a stock flexplate then you will need a spacer on each side of the flexplate. If you are using a Kiggly flexplate then you will only need one spacer on the transmission side of the flexplate. You can bolt this down with the OEM flexplate bolts or you can cut down the manual flywheel bolts to the right length and use them. Torque them down using red loctite.
Go ahead and bolt the Automatic starter plate to the engine.
Now your ready for the transmission to go in. Go ahead and slide the converter on to the automatic transmissions input shaft. Its a good idea to pour a half quart to a quart into the converter if there is no fluid in it before putting this on the transmission. When you slide the converter on you will need to spin it and wiggle it some to get it to seat all the way down into the pump and engage all of the splines. There should be about an 1/4 inch gap between the bell housing mating surface and the pads with the bolt holes on the converter.
The transmission is a bear and if you have a stock front sub frame it will make things tighter around the diff housing on the back of the transmission. The lower radiator hose and stock lower intercooler(if you have one) pipe will make this tighter as well. Once you get the transmission on the dowel on the ears of the block go ahead and put in a couple of bolts in on the top. Please ensure that the transmission does go up against the block when doing this. If your converter is hitting the flexplate or you have a rough dowel pin on the block or a binding issue then DO NOT bolt the transmission in to try. Chances are you will bind something up and break a bolt, one of the ears on the block or the transmission case itself. You can also damage the transmission pump as well. When you get the transmission bolted on to the block you should be able to spin the converter relatively freely without rubbing. This is how you line up the converter bolts to the flexplate.
Now is a time to go ahead and put the transmission Mount and bracket bolted in.
Next comes the converter bolts. There are several options you can use for this and i will not cover them here. Put the chosen bolts into the converter one at a time. Use red loctite here as well and torque them down.
Go ahead and put the transfer case onto the driveshaft then push it up onto the dowels of the transmission. Make sure you have the right PTO shaft or this will not work. The shaft should match the transmission and the splines should match the transfer case splines. You can buy automatic transfer case bolt kits as the manual ones are different.
Now would be a good time to hook up the speed sensor on the rear of the transmission.
Now its time to go ahead and unhook and remove the clutch slave cylinder and its lines. Bleed as much of the fluid out that you can. I cut mine near the strut tower on a high point and cut it again on the firewall at a high point located behind where the battery sits. Take each clip off that holds the line one at a time and pop the line out and put them back on one at a time. Next remove the two nuts from the clutch master cylinder.
Now there are only 2 things left under the hood to do. You can do them now or do them whenever you want. Wiring and transmission cooler still needs to be dealt with. I did these at the end personally but you can do this at your leisure. Your not 100% done still as you will need to be under the hood to deal with the brake booster and master cylinder during the pedal swap.
This is going to be a pain in the ass. There is no getting around it. Ive seen it said that you should start here because if your going to give up. This is where it will be.
Start by taking off the kick panel under the steering wheel. You will also need to take off the steering column covers. You will also need to take out the molded plastic ducting under the steering wheel to get them out of the way. You can also unbolt the steering column at the joint by the firewall if you want but it can be done without disconnecting the wheel as well. Then you can start removing the cotter pin in the brake booster on the brake pedal assembly and the clutch pedal assembly. Start unplugging the clutch switch and a few other things under there that you see needed. Then start unbolting the clutch and brake pedal assembly. If you already unbolted the clutch master slave then you might want to have someone hold it in its mounted position so you can remove the clutch rod. Then remove the clutch master cylinder. Go ahead and remove the brake booster boot now. You will need to ensure the 4 nuts around the brake booster are removed then in the engine bay you will want to start to wiggle the brake booster towards the front of the car. You will likely need to slide a pry bar behind it with the end up against the firewall and pry it forward. BE CAREFUL WITH THE BRAKE LINES! The brake lines can handle this movement as there is slack but dont be careless and break one or crack a fitting. There is a gasket between the booster and the firewall. This needs to stay on. Be aware of this before putting it back together! There is 2 bolts holding a set of relays up under the dash. Take them out and move the relays out of the way so it doesnt get damaged. Go ahead and bend the piece of sheet metal that the relays bolted to so you have room to get the pedals out. This is no big deal and will bend back, it is required though. If you have a buddy helping you have him pull the booster forward while you wiggle the pedal assembly out. This is going to be a squeeze and kind of like a puzzle. You can remove some brackets like the clutch pedal bracket to help make it easier as well. It will likely take you around 20 minutes to figure out how to get it out. Yes its a pain in the ass but this is the worst part of it. Once you get it out then go ahead and put the automatic brake pedal assembly in. This will take some shoehorning as well but it will go in alot easier then how the other came out. Then start putting it back together. Before putting the ducting up and the kick panel you can do the shifter and cable.
Before you button up the bottom of the dash go ahead and unbolt the manual shift cable from the firewall. Then go ahead and take the two side panels off the side of the shift tunnel and the top of the tunner that has the shifter hole, the little pop up storage and the ashtray out. Go ahead and remove the shifter cable clips and start pulling the cables out of the shifter by removing the cotter pins. Pull the cables out through the drivers side where the side tunnel cover is and they will come out. Go ahead and unbolt the manual shifter and take it out. Now you can bolt the automatic shifter into the car. The hole the manual transmission shift cables go through the body of the car are not where the automatic shift cable exits from the factory. The shift cable goes through the top of the tunnel where it comes out by the front cross member and up to the transmission. Its a pain in the ass the cut that out and make it work like stock then have to cover the hole the manual cables go through. Some people just run the cable and zip tie the cable to the area where the ECU mounts. I was able to pull the boot off the bottom of the manual cables. Then one of the cables will pop out of the grommet. You will need to cut the other one out of this grommet. You can then wrap the grommet over the auto shift cable then slide the boot onto the grommet and this will keep it tight. Then take the plate and put it over the grommet and bolt it to the body. This will nearly seal the hole. You can dab some silicone into the remaining open hole in the grommet to seal it up once its mounted. Your cable will be tight. This is because the cable is slightly to long for the route that it takes to get to the transmission. The shifter still works fine. Once this is done you can button up under the steering column. There is wiring to do with the shifter and under the dash there but its still accessible with the kick panel and ducting reinstalled. I would leave the top and both sides of the tunnel off since there is a connector in the shifter that needs to be hooked up to overdrive / 4th gear to work. Also there is a Eco/Sport switch that goes into the top of the tunnel cover that needs to be hooked up or hot wired. If you are manually shifting the car or have a ratchet shifter then none of the shifter tunnel applies and you can reinstall all of that.
This is easy especially if you have done a 4 bolt swap before as its essentially the same thing. If your retaining axles then all you need to do is replace the manual rear differential with the automatic differential. There is truly no need for me to explain this. VFAQ has an article on doing a 4 bolt swap that is way better then i can write. So just use their writeup to guide you.
Main article: VFAQ - 4 bolt swap