A T45 swap is the cheapest way to get a stick in the car and working. The T45 is a good strong trans, with the only real weak link being the 3-4 shift fork. There are companies that make a billet steel replacement shift fork, but that basically requires rebuilding the transmission to replace it. The other disadvantage of the T45 is the shifter location being too far forward, which requires either fabricating papa john's extension box, or cutting a hole in the floor for and making a remote mount shifter. As for the crown vic driveshaft, a stock civilian crown vic steel driveshaft is the right length for the T45 swap, but the police driveshaft is 1" too short. It will physically work to move the car, but it is not ideal. If you want an aluminum driveshaft, you will have to have one made, or get a MarkVIII shaft shortened. The length you are looking for is 56.5" centerline to centerline. For actuating the clutch, there are a few options. I was the one who figured out the S10 slave, and you need one for a 94/95 4-cyl S10. This will require making a bracket to bolt the slave to the side of the trans to push on the stock mustang clutch fork. Another option is a pull type slave, which is more expensive, but won't require any bracket to be made. Another option is a hydraulic throw out bearing mounted inside the bell housing, but I don't recommend that due to if anything goes wrong, you have to drop the trans to change it.
Next up on the trans list is the 99-04 TR-3650. The advantage of this trans is no more 3-4 shift fork problems, and a synchronized reverse. Installation is exactly the same as the T-45 with the added expense of needing an extended range speedcal to make the speedo read accurately.
Next up would be the 05-10 Mustang TR-3650. The biggest advantages to using this trans is ease of install. The 05+ Mustang shifter will land exactly where it needs to be in our cars, and the stock Mustang hydraulic throw out bearing can be used with the stock SC clutch pedal and master, making it literally a bolt-in swap. The downfall to this swap is cost. In addition to still needing an extended range speedcal, you will also need a custom fabricated driveshaft, as there is no stock application that will come close to working.
Next on the list would be the various 6-speeds. A T-56 has been done a few times, but for the cost and difficulty of swapping it in, really isn't worth it. The TR-6060 out of the 06+ Shelby GT500, as well as the Getrag 6-speed in the 11+ Mustangs both should swap in just as easily as the 05+ TR-3650, only the trans itself would likely cost more.
-91 Cougar LS, coming soon, complete overhaul
with a 427" Windsor.
-90SC 5-speed, MP2, coated rotors, double intercooler, 15%OD, ported heads, comp stage 1 cam, 85mm TB, 90MM LMAF, 80# injectors, soon to be transplanted into...
-90 XR7 5-speed black on black w/sunroof
-98 Mark VIII LSC, Procharger P600b, TR3650 swap and 3.73s.
-70 Torino GT Fastback project car. Needs EFI and a manual trans, but I'm not sure what motor to go with yet.
-"Your buddy Mike is INSANE!" -ClintD's dad