I guess what you are paying/paid depends on what exactly was done and may or may not be fair. If you could, post exactly what was done. Depending on what exactly was done to your engine would determine where your $6000 went. See what the breakdown is. I would expect for $6000, new name brand quality rods, pistons...essentially all hard parts replaced with name brand items.

The last 400 Dave prepped for me 4 years ago was roughly $4100....jobber cost (his cost) on parts. One can assume a fair price for R&R on the engine and assembly...I believe Dave charges $400-500 to assemble a long block. I also believe a fair estimate to remove and replace an engine would be $500. I disassembled my engine, took it to him and did the following..

Block gone through, degreased, baked, blasted, bored, aligned honed, decked.
Crank polished, rotating assembly balanced
Heads cleaned trued
Heads SERDI cut
Pistons pressed on rods

New Ferrea valves
Comp Cams 995 springs, locks, retainers, cam.
Harland Sharp rockers
Scat rods
SRP pistons, rings
Clevite bearings, Melling pump, gasket set, pushrods, lifters, timing chain,
Pertronix kit, existing distributor, new gear.
Rochester rebuild kit.

Heads were assembled at shop, I assembled the block and rebuilt carb.

Consider that a shop more than likely has to farm out a lot of this work and you will be paying a premium over what the shop has to pay due to the reality they have to send out a guy to pick up parts, drop off a crank to be turned...take the heads to be worked on etc.

Just food for thought, maybe lesson learned...depending on what a shop says that needs to be done...and if extreme...next time I would do all of the prep and disassembly...take it to a PONTIAC builder...have him assemble the entire engine and drop it in if you are not comfortable doing such.