Setting up the gears in the diffs is best done by an experienced person, bench labor is about $150 plus the cost of gears to do it.  BEnch labor means you would pull the 3rd members and take them to a shop, and then install them yourself.  This save you from paying a shop to spend their time or your money doing something that you can do in your driveway, it is about as hard to remove a 3rd member as it is to change a tire.  You can also order third members from shops like Marlin's, that come regeared, or regeared with a locker.

IIRC, Toyota used a different 3rd member housing for their 4.88 3rd members, so after market gears wont fit.  It wouldn't be an issue if you were to buy a set of factory used 4.88's and ran them until you were ready for 5.29's and lockers, you could easily resell them, and either make money on them or at worst break even.   

If it is as clean in person as it looks in the pics, runs/drives well, and the seat covers are there just to protect the seats, $5500 wouldn't be outside the market, you are also getting extras like the tube doors and some type of extra cover for when the shell is off.  It says it is unpainted, not sure if he means the canvass bikini top or some type of hard top or half shell.