Originally Posted by macgyver35

Go ahead and replace your heater core while you're in there, especially since hotter weather is coming and you will presumable be using your newly repaired AC. AC load will test any weaknesses in your cooling system, and heater cores are common failure items.

Also, check the operation of all of your air plenum control doors/flaps for proper operation, binding, deteriorated seals, etc. Try www.heatertreater.net for common repair kits, or a JY or the stealership.
This is also a good time to give the inside of that plenum a cleaning, as best you can, especially if you notice any funky smells when first turning on your heat or AC.

You may want to go ahead and drill a couple of holes through the firewall and install rubber grommets while it's easier to do if you intend to ever run addition electrical accessories with switches in the cabin. Lights, alarm, on-board air, etc. Just dab a little bit of silicone caulk over the center hole of the grommets until you are ready to use them.

Arm yourself with zip ties to secure wiring looms during reassembly, and also with a couple rolls of cheap foam rubber self-adhesive weatherstrip as well. The weatherstrip (Home Depot. I recommend 1/4"-3/8" wide and 1/8"-1/4" thick. about $3 for a 25 ft. roll) can be used between several of the plastic dash parts as they go back together to prevent rubbing and all of the creaks and squeaks our Jeeps are known for. You'll see places where the factory installed felt or rubber bushings for this same purpose. Some may be cracked, brittle, missing, or worn through. Use you judgement on where to apply.

Lastly, on some years, the condensation drain for the AC that passes through the firewall is known to leak back into the cabin. My '02 TJ did this badly. My fix was to glue a 1/2" or 3/4" PVC elbow from Home Depot to the end of that drain pipe so that it exits in a downward position, rather than straight out. I've found that the straight out approach by the factory can allow for easy clogging of the exit tube with mud/dirt, and can also allow air pressure during highway speeds to blow water back against the firewall where it will leak in between the firewall and the foam gasket they put there. That 25 cent part and some clear silicone around where you see the factory gasket for the drain tube fixed my soggy passenger floorboard for good!