I'm not 100% sure...But I don't think that the 5.0L Coyote will bolt up to an E-4OD transmission. If you go that route I suspect you will probably have to get the engine and transmission as a combo. You might have to check with Ford parts to get a 6R140 tranny...But I would also check junk yards....These 2011's have been out on the road for about a year now...Chance's are someone's wrecked one with the 5.0L/6R140 still intact.
I just picked up a magazine ("5.0 Mustangs and Super Fords", Feb 2012) while grocery shopping last week. They're running a series of articles about swapping a 5.0 Coyote into a 95 Mustang originally equipped with the original pushrod 5.0. This got the wheels spinning in my head about swapping one into my 78 shortbed.
They used a T56 Magnum 6 speed manual trans with an adapter kit from AMP Performance.
I'm sure this will be another one of my "daydreams" and will probably be way beyond my budget, but I'm still going to compare costs etc. I saw a computer and stand alone engine harness from Ford Racing for a little over $1000 if I remember correctly.
Looks like it took a while for you to get an answer.
From all of my reseach it looks like the new 5.0 and 6.2 have the same bellhouse pattern as the MOD motors. I haven't had a chance to get an engine out of a chassis and check yet so take this with a grain of salt. If this is so then you have a bunch of options as any of the autos and manuals from the F150 and SuperDuties could work for what you're trying to do.
It would seem that the easiest way to do this is with a manual. You can get the stand alone kit from Ford racing to run the engine and use a 5 or 6 speed from a 4x4 5.4 or V10 Super Duty. You could use a E4OD or 4R100 but then you'd have to have an aftermarket controller for the trans too.