If you go with the basics, of 5140 RPM forged rods & SP forged pistons, with a Summit cam kit, and a good valve job, don't think you can have it built correctly, for under $3000, unless you do some of the assembly work yourself, or have a friend who'll help you, for free.
Len Williams was mentioned. While you're searching prices, better include Len's crate engines in your search. He builds good engines, and supplies the core, for less than MANY shops charge to build, using your core parts.
Len's cast rod 400 is $4000 + shipping. I assume he can add forged rods for a couple of hundred more.
400 Long Block
Or you can buy just a shortblock, and have your heads done locally.
400 Short Block
455 Short Block
pontiac crate engines
Old stock valves can break, wiping out your engine. So you probably should include the cost of new one piece stainless valves, in your cost. But, you said you weren't asking about what parts to use--OK.
"...this is not about should I use forged or cast pistons, forged or factory rods, iron or aluminum heads, flat tappet or roller cam, cast exhaust manifolds or headers...What is a good price for an engine rebuild? How much should I budget?..."
I personally don't see how you could possibly expect to get an accurate estimate of the cost of a build, without knowing what parts you plan to use. For example: forged parts cost more than cast parts, roller cams cost more than flat tappet cams, new SS valves cost more than using the stock valves that are already in your heads, etc, etc.
Also, some shops, like Len Williams, bore and hone with a torque plate, and know Pontiac engines. MOST local shops build mostly Chevy engines, do not even have a Pontiac torque plate, and know very little to nothing about a Pontiac engine. I know 1st hand how bad a Chevy shop can mess up a Pontiac engine
So, given the question you've asked, I don't see how we could possibly give you the exact answer you're lookin for. But, good luck with your build, anyhow !