My take: You should add mods as solutions to real problems, one at a time.

For most people, AT tires are obviously the first mod because stock tires severely limit what you can do with your 4WD system. That pretty much blows your $1,000 right there.

Beyond that, your next mod depends on the next thing you want to do but cannot with a stock SR5. Maybe that's a lift, maybe skid plates or sliders, maybe a winch.

But the reality is that all of those are going to cost many $1,000s installed, unfortunately, so choose wisely and spend your money on things that solve your particular problems as a 4runner driver. That will be very different depending on where you live and what you use your truck for.