It's not horrible to do, you can either tape the glass in the Up position after you unbolt it from the regulator; though if I remember right I ended up having to remove it completely to get enough room to work in the door last one I did (it's been a year or so). Removing the glass will require unbolting the spoiler assembly from the door and removing the plastic trim on the left and right side of the door, it's a bit of a tedious affair, but doable.

As for the regulator itself, it's not clearly stated in the instructions, but you have to kinda fold and unfold it in and out of the hatch opening to get it to go in properly; it's a bit of trial and error so take a picture before you remove it so you can get a rough idea how it goes back together.

I would also make sure you have a new regulator and a motor, it's possible the cables could have burned out the motor or shortened it's life by overheating it (should be protected, but old vehicles and all that). I would also highly recommend replacing at least the exterior belt moulding that goes on the hatch and seals with window and interior of the rear hatch as that will lessen the likelihood of debris, moisture, and such getting in and gumming up your cables again (at least for a while... it's an often overlooked item that I am sure is very brittle/poorly sealing on many 4Runners after a while).