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.
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 '87 GT in process, including GA / Seville brakes, Poly Suspension, '95 3800 Series 1 SC ( 225 hp )  4t60e.