I rescued my 4runner from a dealership about two years ago so I can speak from my experience only.

If it is running good (smooth idle, etc) I'd just do a good oil change on it, and an intake filter. I went with Napa Gold on the filter.

First thing you should do I check the age of the radiator. If it's the original, replace it with a new quality one. I went with the expensive Toyota OEM one from the dealer.

Also LBJ should be inspected by someone with enough experience to determine their condition.

After all that checks out, I would set aside a couple of hundred for future unexpected stuff.

After that see where your budget sits. Maybe you get out cheap and still have $2000.

Tires and a decent lift will blow that very quick.

The rack will probably have to wait, but at least you got the maintenance stuff done, and the lift/tires will get a 3rd gen pretty much anywhere you wanna go.

You can also just select the shocks/struts you desire and run some used coils from a FJ or 5th gen for a while to give you enough room to clear 32's, and freshen up the suspension.