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.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.