Well, there's no such thing as a cheap and reliable RB rebuild. Given that aftermarket rods have also come down in price, I would factor those in the rebuild. So essentially looking at new pistons, rods, bearings, crank collar, machining, assembly and new fluids and service parts (gaskets, hoses, belts etc).
My "thumb suck" is that you should be allowing for around $6 to 8k including removal and fitting.
I'm assuming that you have some steel wheel terbs already fitted and that these are in good nick as is your clutch, gearbox, transfer case............you get the idea - welcome to the (expensive) world of GT-R ownership!