Wow that's a clean looking 3rd gen man! Congrats. I think others here will agree that modifying these trucks is a slippery slope, a very expensive but fun and fulfilling slippery slope!
It all depends on what you plan on doing with the truck and how much time/money your willing to put into it. If it's going to be a daily-driver with some light off-roading mixed in, I would first remove the running boards, get some 32" all-terrain tires, and maybe perform a mild lift(2 or 3 inches).
You will see lots of guys on here that go BALLS OUT with their trucks because they do a lot of hard wheeling and rock crawling out west. If you don't plan on doing a lot of hardcore off-roading, you probably don't need 35" mud terrains with 5 inches of lift and full armor (i.e. bumpers, skids, sliders), unless you're just rolling in the dough and don't give a shit about gas mileage or on-road manners

. Tailor the truck to your needs!
Before you start dumping money into the truck and making drastic changes to it, make sure everything is mechanically sound. There are some great threads on here that cover all of that. Do your research and take your time!
Start by reading this:
3rd Gen 4Runner Buyer's Guide
If you interested in lifting your truck, read this:
3rd Gen 4Runner Lift Information and FAQs
If you are ever looking for specific information on a topic, try using the search feature before starting a new thread about it. Chances are the topic has already been beaten to death in previous threads, just gotta fine em! But don't be afraid to ask questions, that what this forum is for!
Good luck!!!