Have yet to see it done, but a truck bed liner might work, just section out the front portion for it to fit if you want a something up against the back seat.

Most use aluminum or wood to redo the the side panels.


https://www.yotatech.com/forums/f116/1st-gen-4runner-cargo-panels-224021/


https://forum.ih8mud.com/threads/replacement-interior-panels-1st-gen.451594/

If your original panels are intact but cracked/damaged, you can repair them using fiberglass and bondo, that is what I did to repair the x-cab panels in an '84 I restored a few yrs ago.  Used the fiberglass to reinforce the back side, and reform the areas that had pieces missing, the bondo/sand the front side to refinish.
 

Depending on your planned use, you could also do something like the "carpet kits" that used to be popular in trucks.  I usually build them with a tool box in one side.


You could also have them sprayed in Line-X.

Whatever you go with, would suggest lining the rear body with some sound deadening material to quiet things down, or insulation if you might use it for camping in.

If you mean cutting down a bed liner, just use a die grinder or 4"grinder w/a cut-off wheel, tape the area that needs to be cut so you can draw a line on the tape, the liner cuts pretty easy, just have to deal with plastic debris and fumes, so wear a dust mask.

Another option for a drop in liner would be to fabricate your own liner using light weight sheet metal or aluminum and rivet/glue it together, than have it sprayed w/Line-X to make it durable, might even be be able to use something light posterboard and have both sides sprayed.  When a buddy owned a Line-X shop he sprayed all kinds of stuff with it from empty soda cans to powdered doughnuts, whatever it was sprayed on damn near made it indestructible.