There are two sets of bolts you need at the back of the motor. The first set is the flex plate to flywheel place bolts. They are lower profile but not what you would consider low profile and you can't substitute normal grade 8 bolts for two reasons. The first is the oddball length and the second is they are place bolts with a special head configuration to prevent loosening when torqued correctly.
The second set of bolts holds the torque convertor to the flex plate and they need to be the ones designed for that application as well for similar reasons.
As far as the wiring goes, you may or may not have the short adapter to hook up the harness for the NSS and TCC switch for lock up.
The 2002 need to have the harness from Vintage Parts purchased and used. It will plug into the adapter harness that the reverse light switch plugs into for the manual. Other years just have the correct harness folded back and taped in place.
You will also need the firewall block off plate for the clutch slave and master. Don't get sucked into the higher prices on Ebay, it is about a 10 dollar part at the dealer.
For the center console, you will need the auto shifter floor plate for the auto and the shift indicator bezel. The bulb holder is taped back along the harness under there and a 194 bulb will need to be plugged into it and then stuffed into the bottom of the bezel to light up the selector when the dash lights are on.
The auto shifter can be had at the dealer or Davey's and you will need a new shifter cable. The one from a Cherokee will work but I don't recommend it. The TJ version has a section of heat wrap on it where it goes by the exhaust manifold and the XJ version doesn't which cooks the cable housing and then it will break.
A TV or kick down cable will need to be installed. When you install it, you also remove the return helper spring from the throttle body lever and discard it. The TV cable has a spring on it at the trans bracket.
When you install the new trans mount, you will need the square adapter plate that bolts to the trans skid. The bolt holes are there and use carriage bolts pointed up with the nuts on top. It mounts over the other set of holes in the skid that the manual mount is not using.
The actual trans mount is the same but the adapter plates that bolt it up to the trans are different between the two.
The t-case shifter needs to match the one from the trans due to the different lengths. The 32 is the shortest trans Jeep used in the 6 cylinder TJ's so the t-case is further forward which also makes the front driveshaft short and the rear longer. The t-case bell crank tub side bracket is the same and the difference is made up with the bracket on the trans and the two linkage rods.
The bolts that hold the trans to the block are not the same as what holds the manual to the block and you need the motor plate with inspection cover for the plate.
It may have been mentioned but I skimmed a lot of it, but use ONLY a Mopar radiator with the auto trans cooler built into it. If it hasn't been done in awhile, now is a good time to do a flush and get some new coolant in there while you are doing the radiator swap.
The absolute hardest part of the swap is loosening the exhaust so you can snake the cooler lines between it and the oil pan. Try not to cobble together the cooler lines and only use OEM if possible. There is a check valve in one of them that prevents torque convertor drain back which delays the shift into gear after it sits overnight.
If you don't locate a PCM in time before the swap is complete, you can run it with the manual PCM. It will throw a CEL at key on start position due to not seeing the TCC lock-up circuit. It will run well enough to test the trans. Don't run it like that for long as the CEL will stay on and it may need to be on for something else that is more important that you won't know about.
The trans requires ATF+4 fluid and roughly 10-12 quarts of it. Now is a good time to do a deep pan swap and replace the grommet at the base of the dipstick tube where it enters the trans. They tend to dry out if the trans has been sitting and will weep. If you notice any holes in the trans where the pan bolts up that are a bit wonky, I have some Timeserts I use to fix them. They tend to strip out very easily in the cast aluminum. Use the re-useable pan gasket that is the hard plastic with the raised ribs. They work perfectly every time and are worth the money. The deep pan uses a drop down extension for the filter so don't get a deep pan kit without one. While you have the pan off, weld a bung in it for a temp sensor and run a temp gauge. You will or should use a small cooler in front of the radiator to aid with cooling the auto and plumb it in series with the return to the trans from the OEM radiator.
