I'm going to try and add my opinion without offending anyone, based on past experience building chassis' and such. Mind you, this is what I would do if a customer came to me with an open checkbook, and desired something of my design...feel free to cratique (sp?) me after...
4Runner base vehicle...are there better platforms for a pre-runner?...sure...I would find something with a touch more wheelbase but not too much to make tight turns an issue, and keep weight bias in mind, something like a mid size pickup would be my choice (tacoma maybe?)...but, given the question and proposed vehicle, I would first strip everything from the frame, box the entire length, and get my head pointed in the four link direction...triangulated upper links (wishbone) and parallel lowers, all the same length as the driveline (reduces geometry issues vs long travel)...King coil-overs or Fox bypass type suspension, as long as possible (reduces heat when compared to shorter stroke shocks...more fluid). ****can all four wheel drive equipment, go with two wheel drive stuff (less moving parts to break, and less unsprung weight) , 9 inch ford rear (faster gear changes and durable, plus no c-clips to break 200 miles from nowhere), automatic with low first, and higher 1 to 1 high gear (varied terrain), two wheel drive Ford I-beam front end (PROVEN durability in the desert), with longer control arms for better geometry when swinging through full arc), fuel injected small block Chev or Ford built for durability and torque rather than all out horsepower...about 3 to 4 hundred feet of 1-5/8 DOM tubing to hold it all together.
Goal of at least 36 to 40 inches of travel front, and a minimum of 40 inches rear, with a weight bias of 40/60 to the rear (keep the rear tires on the ground as much as possible). 400 to 500 hp is a reasonable number to shoot for and keep good durability, top speed of about 100 (given the aero of a 4Runner is like a brick, and keep the COG as low as possible.
Pre-runners travel the course at lower speeds, so the truck "feels" all the terrain rather than skipping over it, and keep in mind, we havn't even gotten to stuff like controls, or electronics (score now requires GPS and radios that can cost mid 4 didgits just to purchase, let alone install)
This is just my idea...I've been to Baja twice with two different teams, and if you're talking a real deal pre-runner, expect to write checks for about 80 to 100 grand if you do the labor (doing everything right and safe), 175 to 225 if you have someone build it for you...but it's a fu**in' blast when you get there.