I wouldn't even say that it would cost $3k. $1200-1500 for the regear, including parts and labor. $120 for the JKS BL. If you have a jack, block of wood, and a wrench set you can do a body lift install and save more money. Hopefully removing the 3" one won't be too much trouble. Also I would suggest a MML as it helps with driveline angles and vibrations for that 4" lift.
Well, jp2611 said $3k to be "set". That says to me to install the smaller BL, a MML, a SYE kit and regear. Which would cost you around that much for a shop to do it all.
I'll also throw out that it is much cheaper to buy a jeep modded and freshen it up than to buy a stock jeep and mod it. Jeep mods translate poorly to trade in value. I still so wish that I got the TJ with the chevy 350 in it (also came across one with an LS2). Damn you emissions tests in my county!
'03 TJ Sport
/ D30/Ford9 / 35x12.5x15 KM2 / D window black steel 15x8 wheels / 3" custom long arm lift / SYE & 1350 DS / JKS BL / 1" MML / Smittybilt's front bumper, Tube fenders, Rocker guards, and rear bumper / High Rock Tire Carrier