I just did this swap and wanted to throw in a word of caution regarding the rear disks. For the record, my 4Runner is a 2006 Limited that had the upgraded 'Sport Brakes'. I used 5th gen (2010) TRD pads along with Napa remanufactured calipers and ultra premium coated rotors. The fronts had zero problems.

After assembling the rear I had a clicking noise coming from the passenger side of the tire at all times exactly once every rotation. Through troubleshooting, I found that-

-It only happens when the lugs are torqued on.
-Removing the caliper doesn't fix the problem.
-Backing the parking brake all the way off doesn't fix the problem.

After swapping back and forth a number of times I noticed small play around the hub with the new rotors that wasn't there on the old. Looking up the specs the center hole is slightly larger on the newer rotors. I swapped to new 2006 rotors and the problem is resolved.

I believe this extra play around the hub allowed the rotors to get locked down off center. This wobble in the rotation was binding at one point on the brake shoes, but only one and only for about a cm patch. I never use my parking brake and believe if I did and the pads were worn even slightly more the problem would not have surfaced. In that case, the rotors would still be slightly off hub centric though.

Use 4th gen rear rotors