This is just a rough estimate ( so don't kill me over being a little off!!), based on what I am doing. A lot will depend on what Donor engine you get, and what other items you can get from a donor. I would say a low of $2K to a medium of $4k, to a high of $6-7K if you have it done.
I bought a wrecked Riviera, so I got the engine, trans, wiring harness, ECM and axles. I parted out the balance of the car, and actually made money on the deal. If you have to buy an engine drop out, seems like the going price is $800-$2000, depending on year and what you get.
If you can do your own wiring harness, and you get the donor harness, the wiring is pretty inexpensive- maybe $100. If you buy a ready to install harness, budget $500-$650
Motor , Alternator and Transmission mounts can cost from $100 - $500, depending on how much you can fabricate vs purchase.
If you are staying ( or going) manual, you can add another $700+ for Clutch and Flywheel. If you use the donor trans, it's cheaper. May only need some mounts, and maybe an Axle or 2.
Exhaust will cost about $200-$500 in parts, plus the labor to fabricate and weld.
ECM Programming can cost around $100. You can do it your self if you have HP tuners, but that cost's another $500+
Figure at least $500 more for other stuff, like radiator hoses, Spark Plug Lines, fuel lines, cold air input, etc. That figure can easily double ( or more) depending on how clean you want to make your install ( things like replacing the firewall insulation, replacing engine gaskets, rebuilding supercharger bushing, etc)
One other thing I did was to prepare the vehicle for the increase in power- Better brakes, rebuilt suspension w/ new bushings, new cradle bushings, New radiator, Battery Relocation. This can add another $1000 to the total.
'87 GT in process, including GA / Seville brakes, Poly Suspension, '95 3800 Series 1 SC ( 225 hp ) 4t60e.