Doing an auto to F 40 stick swap is a big job. You will need the transmission, the clutch, the fork, a flywheel, throwout bearing, shift cables, modified shift arms, the shifter itself, trans cable bracket, clutch pedal/bracket, the safety switch, the back up light switch, the clutch master cylinder, the slave cylinder, the hydraulic lines and some hardware. Its been done before but I would consult with someone that has completed this.
A much easier solution that gives you a forth gear is to bolt in a 4T60 automatic but if you have to have 6 speeds and a stick then start gathering up all the parts and be prepared to do some fabrication and hours of work.
" THE BLACK PARALYZER" -87GT 3800SC Series III engine, custom ZZP /Frozen Boost Intercooler setup, 3.4" Pulley, Northstar TB, LS1 MAF, 3" Spintech/Hedman Exhaust, P-log Manifold, Autolite 104's, MSD wires, Custom CAI, 4T65eHD w. custom axles, Champion Radiator, S10 Brake Booster, HP Tuners VCM Suite.
87GT - ALL OUT 3.4L Turbocharged engine, Garrett Hybrid Turbo, MSD ign., modified TH125H
" ON THE LOOSE WITHOUT THE JUICE "