You can do tons of stuff. There are a lot of mods (performance or style) you can do...
Painting the rims saves mucho bucks if cash is tight, but if you got the $$ for rims, it's up to you. It's your 4Runner! I agree, no bigger than a 17. I'm running Hankook AT 265/75/16 on stock rims (not rubbing) and they are going to be painted soon.
Blacking out the emblems is cheap and looks good. Looks good on my Silver paint..
You can replace the bulbs in your gauge cluster with LED's for a different look too. I just put blue LEDs to light the back of the gauges, changed the Check Engine light to a red LED, changed the turn signals to blue as well. I still need to change the light in the key ring to a blue LED as well as the shifter to a blue LED. Possibly one more blue for the ashtray light too..I ordered them from superbrightleds.com so if you want the sizes I used, let me know.
Performance mods - deckplate mod, isr mod, o ring mod. Just do a search and you'll find tons of mods people have done.
Congrats and welcome to the club!