Considering you have done all the right maintenance stuff your probably looking for the fun part. Being a kid you can never go wrong with altitude, but don't skimp on the right parts, lift it right and you will be happy for a long time. Next would be tires, now with your new lift tires seem like the next move, but remember bigger tires mean slower truck, so be realistic in what you want, common tire size once lifted are 285/75/16. I must say they look nice with a 3" lift but they will also mean more stress on the motor, so you might want 265/75/16 which are just under 32" or you can go for some skinnier at 255/70/16-or 255/75/16 I never remember that middle number.
As a kid I always drove like a bat out of hell, and knowing what I know now I would do one important thing to my truck and that making sure she can stop. So look into the tundra brake upgrade or (TBU). Basically it is what it says, you can install the front brakes from a tundra onto our 4runners and it's got mean stopping power, by far one of the best things you can do for safety reasons.
Next for me would be protection, bumpers front/back and sliders.
Sliders are what go in place of your removed runningboards. They protect you from any body damage that can push your underside into your door jam and make it impossible to open your doors, so yeah they are very important and should not be skimped on.
TBU is about 500-600
Lift a good one, is about 800-1300 Toytech, Sanora steel, OME
Sliders prefer they be (DOM) about 200-500 depending on builder,
4xinnovations, Stubbs, are just a few of the many out there.
Your very smart for taking care of your rust issue, these trucks will stay running for you a very long time as long as you be nice to them and take care of them. Now that doesn't mean you can't have fun and beat them up because many of us do beat them up, it's just you need to do the right things before you do the dumb things. Lift it, protect it, stop it, and you will have many years of abusing it as long as you maintain it. And remember, rust never sleeps so always crawl under it and make sure you know what's happening under your rig.
Good luck, have fun!!!
Be careful, it's not a race car, drive within the runners limits.