Doing the work yourself? Either way is going to probably cost a grand or so, that's with getting the trans (cost will depend on what you go with). You'll also need an ecu harness from a 5spd as well I believe.
It's been done before, try Google searching.
Sent from my SPH-L720 using Mustang Evolution mobile app
It's an easy swap but it will set you back a grand. I just did the swap. It's easy to do. Had my auto side turned off on the Ecu so you don't need a new one. You'll need a new pedal assembly, clutch cable, flywheel, flywheel bolts (auto bolts are shorter), clutch, trans of course, clutch fork, trans mount, trans yoke, a new drive shaft is not necessary.
It'll set you back a grand if you get the trans used. In my experience, it is a crapshoot with a used T-45 and especially a used 3650. You can pick up a brand new 3650 for $1060 shipped to your door and then all the other swap parts to do it right...
-Resurfaced stock flywheel $100
-Shifter $100 used for a Tri-Ax
-Pedal assy is probably $25-$50 out of a JY
-New transmount $100
-Clutch cable/quadrant/firewall adjuster $160
Then whatever tuning the ECU costs or get another ECU for $100 but you'll have to have PATS turned off via a tuner as well.
For 1/3 the price you could j-mod and put a nice Freakshow converter in the auto which will probably pick up a good half a second or more in the 1/4 for a bolt on NA 2V with 4.10s.