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.
Gear ratios are also an important factor.
Depending on what rear gears you're running will make which transmission you choose/ratios in the transmission more important.
1-4 are important, but for cruising 5th (or 6th if you have it) is also critical. If you have 3.73's for example, here's a list of RPM's at speed with a stock size tire.
Stock, 4r70w is a .7 OD, 70mph is 2300 rpm, 75mph is about 2500.
The t-45 has a .67 OD, 70 is 2200, 75 is 2400
The TR3650 (02-04) is a .62 OD, 70 is 2000rpm, 75 is 2200
the 05+ 3650 is a .68 OD, so very close to the T45, 70 is 2200, 75 is 2400
The T56 can have either a .62 or a .5, we already know the .62, so the .5 is 1650rpm, while 75 is just under 1800 rpm. Both of which are too low for decent mpg if my 2002 Crown Vic with 2.73 rear gears is any evidence.
The TR6060 has a .62 or a .5 as well (it's just an upgraded T56, same as the T56 Magnum)
The MT-82 from the 11+ Mustangs has a .65 OD, but has the added advantage of being a much closer ratio with only a single overdrive, unlike the T56, T56Mag, and 6060 which have double overdrives. The MT-82 will get you just over 2100RPM at 70, an 2300 at 75mph
Me personally, if I was going for a six speed, I'd try for an MT-82 or a T56 Magnum. Both are expensive, but the MT-82 has five "normal" gears with 5th being direct drive, and sixth being a nice OD for cruising. The T56Magnum, having two models, one with closer ratios and a .62 OD would be my choice, as it has many advantages, including (if you get the actual T56 Magnum, not the 6060) a mechanical speedometer option. The other OD in the .62 gearset is a .80 to 1, so it's better for lower speeds while giving you a good cruise gear.
My experience with the ford 4.6 is that it's sweet spot for cruising is between 2000 and 2300 rpm. When I had a 2002 Crown Vic, it had 2.73 gears and the .7 OD. I was barely turning 1700 RPM at 75mph, and it got HORRIBLE mileage on the highway. I averaged 20mpg on my trip from Houston to Duluth, keeping to the speed limit the whole time. The only time I got better was one spot in Kansas where the posted limit was 80, so I kicked it up to 85 and I got 24mpg. My other 4.6 cars (1997 Thunderbird stock with 3.27, 1999 Mustang GT with 3.27 and T45, and my current 1997 Thunderbird with 3.73's) get their best mileage between 2000 and 2300. My first Thunderbird would get me 27mpg reliably at 75mph (2200rpm), my Mustang getting me around 26-28 at 75 (2150 rpm) and my current car getting me 25mpg at 65mph (just over 2300 rpm, 70 in my car is 2400, and gets me 24mpg, due to my smaller diameter tires).
So, for the fun driving aspect, any manual will help that. My opinion is that the T56Mag and the MT-82 are the best choices, but also the two most expensive.