@ErikM I'd go full OCD when it comes to a lift. I have been wheeling 20 years and 240,000 miles in that 80 you saw Saturday with a simple bolt-on Old Man Emu (OME) 2" lift and OME shocks. I can run all but the absolute hardest Moab trails and still cruise the speed limit to Baja and back no problem.
I have factory lockers, I like lockers, I rarely "need" them.
I don't know that shop, but the first modification should be the nut behind the wheel (the driver). I run about the same tire size as you mention. I cannot speak to the particulars of lifting a 4Runner but my resources for a 4Runne would be Toytec and Cruiser Outfitters - people who know quirks. Many jeep guys just bolt crap on and hope it works. If not, they bolt on more. Maybe your shop is an expert, I don't know. 3" is a lot of lift.