Replacing a heater core isn't a big deal in a YJ, unless you have air coniditioning. If you have air conditioning the refrigerant must be removed, so the A/C lines under the dash can be disconnected. The only other option that I saw is to maybe remove the entire dash, and that might gain you enough room to fanagle the heater box out of there without disconnect the A/C, I don't know if this will work or not though, so I disconnect the A/C lines.
Only the center section of the dash and the glove box needs to be removed on a YJ to get the heater box out. The blue arrows point towards screws, the red circles are tabs that are behind the other dash pieces. The glove box just has screws at the top, and a few bolts along the bottom of the glove box door, inside near the hinge.
I chose to remove the radio, and center gauges to get a little more access:
On the firewall side, there are 4 nuts you need to remove. The blue arrows point towards the nuts that need to be removed. The one down low was near a brace, you'll see it.
Once you get all the nuts off, you can disconnect all the control lines from the other side. You'll find three cables go to the heater box. One for the hot/cold selector, one for the vent/recirculate, and one for heat/defrost, they all use push nuts to hold them in place.
These push nuts, you can just wobble off, be gentle with them, otherwise you'll be making a run to the parts store to get new ones. Also be careful when remove the plastic clips that hold the lines to the heater box, they can be very brittle.
You should be able to slide the box out enough to disconnect the fan motor harness and remove the heater box. Be gentle at this point, if the box doesn't want to move stop and figure out why, make sure you removed all the correct nuts, etc.
Once the heater box is out remove the blower motor. Then remove all the small bolts to open the heater box up. Careful with this step the back plate on the heater box should be sealed, so it can be difficult to remove it without denting it up.
Now would be the time to clean the box out, this will help eliminate any weird smells your heater may have.
You'll notice the factory heater core has foam around it to help seal it to the box, and keep it from moving around. This foam doesn't come off very well, but try your best to get at least some of the foam off and place it on the new heater core. I didn't get all the foam off, but I did get some on the bottom and side to keep it from moving around.
Now when you place the back of the heater box back in place, make sure you the door pin for the hot/cold selector and the heat/defrost door are correctly placed, I am pointing at them in this photo:
Now remember you should re-seal this box, this will prevent air from escaping which will make your heater work better. Silicone will work fine for that. Also remember all these bolts and nuts on this heater box are going into plastic, they aren't supposed to be super tight, they will strip easily.