Hello! My name is Dan and this will be my first post on ExPo.
I'm not familiar with 3rd gens, but I am definetly more than qualified to answer your question in a general form.
Because your vehicle is newer than my "84-ish" 4Runner, parts are going to be more expensive. The easiest, and possibly cheaper, form of completing such a task is to purchase a 3rd gen 4x4 4runner that has endured extreme body damage and has been totaled out.
Then you take the sheetmetal tub from your vehicle and drop it on the donor frame and drivetrain. Which engine you keep is up to you. You can go by mileage unless you feel that your knowledge on the current health of your motor is more important.
DMV only works off of VIN numbers found on the sheetmetal body structures, thus you can keep your registration intact. CHP and other law enforcement agencies use VIN numbers from both body, frame, and on some occaisons, engine block numbers during case investigations. So as long as you stay out of legal trouble, mismatched frame and body numbers are irrelevant.
As for my 4Runner, I was building from an extended cab truck. So naturally, a new body and frame were necessary to complete my "truck to SUV" swap. The severe mismatch of VIN numbers ultimately led the CHP inspector to classify it as a "special construction vehicle". Though the title is unusual, it has not held me from obtaining a legal on-highway vehicle registration. The truck is my everyday driver:
For my project, I had to cut and relocate certain frame mounts because the donor frame was a short bed/standard cab frame mating to a 4Runner body. However, for your project all mounting points should match just fine as long as you're using 3rd gen 4Runner stuff.
So, give it time to think over such a project. If you're mechanically savvy, and have determination and EXCELLENT organization practices, it can be done. I have had no issues with doing such major surgery, because I thought and planned ahead and checked every bolt twice.
"Oh what a feeling... TOYOTA!"