You'll need to take the 4runner to a shop that can monitor all tires and axles.
I used Sanders Auto here in Pittsboro and they know their stuff, but not sure of folks over by Raleigh.
Just some general relatively un-educated thought on what to tell an alignment shop to get the results you will need if you are running 33" and bigger tires and doing 2.5" or more lift:
If you bought the rear adjustable later rod / trac bar thingy, then you will want the rear adjusted out so that you don't crab with the front end. This should be done first.
For the front, to get the appropriate caster out to avoid rubbing and be in spec, you will want the following:
Push caster to up to up to 4 degrees and then get the camber back to spec. You are pushing your axle system out first and then as they put camber back to correct, it naturally pulls the caster back a few tenths of a degree or so as part of the process.
You will want to be on the long side of the caster movement as you will need it to clear the rear inner wheel well with larger tires, but, with the lift it seems to make the 4runners feel more "sure footed" to me.
3rd Gen Alignment Specs:
Toe / 0 to .20 degrees
Camber / -.6 to .9 degrees
Caster / 1.7 to 3.2 degrees
If you don't say anything a lot of places will just check caster and then work on the camber and toe. You will rub if you don't push the caster out a bit.
I asked for 4 degrees caster and it came back to around 3.6 degrees - so if you want to be in spec, most likely you can advise to take caster out to 3.5 and then do the camber.
I have plenty of clearance now for the rear inner wheel well, but believe based on all of my reading that around 3.5 degrees may be enough. You may also be limited in what you can get, in which case, you just want them to max it, but also allow for good camber.
Others on here may have experiences. We could always look at my truck, drive it, etc first to see what you think.