Got the itch

The T45 swap is definitely not the sturdiest manual trans you can swap in there, but it is definitely the cheapest way to get a manual trans in a 4.6 tbird, and it is a good trans. The only weak link in the trans is the 3-4 shift fork, which you can get a billet replacement, and then it will hold up to quite a lot of abuse. If you do the swap with a trans that has a stock 3-4 shift fork, then make sure to go easy on the shifts into 3rd and 4th, otherwise it will be a matter of time before it breaks. The only real custom fabrication involved in the T45 swap is setting up the hydraulic system and moving the shifter back. For a driveshaft, a steel driveshaft out of a 96+ non-police crown vic will be the right length, and you just need to swap the diff flange and the T45 yoke onto it, or you can get a custom made aluminum shaft. Other than that, it is all plug and play with factory parts and electronics, and a tune to turn off the auto trans functions in the computer. Considering used T45s can be found for around $250, if you are on a budget, and willing to do some fabrication yourself, the T45 is where it is at. With a little parts hunting, junkyarding, and fabrication, you can get a T45 in the car for under $1000, including the cost of the tune to turn off the auto trans functions.

Using a TR-3650 out of an 05-09 Mustang GT saves you on fabrication because you can use the factory Mustang hydraulic throwout bearing and the factory shifter lands in the right location for our cars. The added expense comes from the trans itself being more expensive, the fact that you will need to have a custom made driveshaft due to the flange style yoke instead of the slip-yoke, and the need for an extended range speedcal to get your speedometer working due to the different style sensor used. However if you can't do any of the fabrication yourself, this may be your best bet since once you have all the parts, it is literally a bolt-in swap.

The TR-6060 would be the same type of a swap as the TR-3650, but with the added expense of the trans being much more expensive.

The T56 would be more along the lines of the T45 swap as far as fabrication involved, but with the trans itself being more expensive than the T45, and I believe you would also need the speedcal. Considering how much easier the TR-6060 swap would be, unless you got a killer deal on a T56 for a 4.6 Mustang, there really would be no reason to swap a T56 behind a 4.6 in an MN12.