I'm not suggesting that this is the best order, but it's the order I took along with reasoning:
1. Tires (first week) - Better traction, sidewall protection (E 10-ply tires), appearance upgrade...
2. Sliders (second week) - Protect the rockers -- plus something of ******* door ding protection on my brand new truck.
3. Recovery gear (shortly after, pre first trip) - MaxTrax, non-kinetic "snatch" strap, shackles, and a hitch receiver recovery bar. On-board air and air-down tools probably go in here as well. MaxTrax, strap, and shackles got used a few times on my first trip while "breaking trail" through early season snow with my brother.
That was it for a while. Didn't have budget for a lift, also wanted to hold off until I "finished" adding weight. Did some functional mods in the meantime: added fridge, cargo management, Gobi rack, etc.
4. Better skids - that first trip did a number on the stock front and fuel skids. Got a full set of RCI aluminum skids during the group buy.
5. Front bumper and winch (waiting for delivery of bumper) - I've REALLY been wanting a winch for self-reliance. I went with a modest SSS bumper to provide a bit of direct protection and to retain the 4Runner look, but still get better recovery points and a place to mount the winch.
5b. Lift (as soon as bumper and winch get installed) - Belly clearance, breakover angle, and dealing with the added weight (and appearance, I mean come on)
One of the decisions I juggled, for my more overlanding needs, was whether the lift or armor should happen first. Arguably with a lift the armor would be less used, but I decided that either way the armor is a required damage prevention measure, even if the armor will see more use without the lift it'll get used either way. Plus adding weight after the lift would require adjustment and possibly even spring replacement.