welcome!
of all the things you listed, and since you are going to be more towards street than offroad Id say go for visual things that will have a major impact.... first and foremost would be rims. I dont plan on changing my rims, but I know that If you really want to change the appearance of a vehicle without much BS getting prettier rims is one way. Knobbier tires, well Im supportive, but I offroad 3-4 times per week and If you arent gonna really be going offroad i think you might be making more of a comfort/smoothness sacrifice than would be necessary. I dont have any doubts about having mud terrain tires, but Like i said, I use them frequently. But that also leaves lots of all terrain tires up for selection.....
Debadging is cool, I havent yet done it too my 4runner, but did it to my previous car and really liked the results. Smoothness is never bad....
Tinting- imho is a NECESSITY. When i ordered my truck i ordered the factory tint AND got 15% on all windows..... sometimes i like to pick my nose/drink a beer/smoke a joint/ whutevar.
I really like the projector/hid headlights of the 06+ but I prefer the SHAPE of the 05- healights.... and as far as ive known it takes a VERY skilled person to make an hid/projector setup happen in a headlamp that isnt initially setup for it.... but the quality of light IS better. If you can afford to do it right than do it, or if you dont care than do it too!
exhaust is FUN. to me I havent a regret about it.....but it depends on the person..... this kind of thing seems to be highly subjective esp. amongst 4th gen 4runner owners :artist:
Lastly, I am powdercoating my stock sport rims SOON. not black but gunmetal..... I like to be unique ( or is it uneek?

) and I think the contrast will be complimentary.
Sorry for the lengthy post, but I just consulted JAH... and am offering honest input. again welcome.