I've been thinking about doing this swap perhaps down the line, what I would suggest is finding a dohc long block if possible, or atleast a short block from a non 03/04 Cobra. Then build on that block, uprgrade to forged internals, upgrade the heads intake if you have the cash, then slap a blower or nitrous on top of it. Your 3650 tranny will work with this combo, but may need to uprgrade your clutch and possibly some other small parts. If money is an issue you should just have a built 4V in N/A form, and then when the money allows it go further with a blower or nitrous. I'm not exactly sure why the swap isn't done more often than I see.
However, you may want to stop and consider what your goals are for the car. How much power you want, budget etc. A 4V would be nice, however the 2V has been proven to make alot of big numbers itself. Depending on your budget and desires you may want to look into the differences between a 2V build up and the 4V swap.