It would cost as much as a Coyote swap and the T-56 is not worth swapping for you. Your 5 speed has the same power holding capability and final overdrive as the T-56. 6th gear is .62 which is what the 02-04 5th gear is. You gain the .80 5th gear going to the Termi trans and you LOSE the nice steep 3.37 first gear of the 3650.
As far as the motor, just Coyote swap it. To answer your question... for just the motor swap plan on $10k or so doing it right for a lower mileage motor worth swapping. So it would very likely be cheaper to take that $$$, sell your 04 and then buy a Termi or a 11+ GT outright.
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 ****.