Keep: Engine, Trans, PCM, Cruise Module, All underhood engine wiring, AC Hoses from Compressor, Dogbone mounts ( just in case you can use some of it), Transmission, Axles, At least 1 foot of exhaust pipe and connection at manifold. Take more exhaust pipe for practice welding if you are going to build your own exhaust. OBDII connector, any weatherpack type relays underhood. I try to get as much extra harness as practical, since I'm always looking for extra wire to re-wire / extend something. It's nice to have the right color wire available.
Consider selling some of the other parts from the car on Ebay to help recover some of your investment. I've made some good money doing this. Sort of a challenge for me to see how much I can sell.
'87 GT in process, including GA / Seville brakes, Poly Suspension, '95 3800 Series 1 SC ( 225 hp ) 4t60e.