Actually the BW4406 will no work on your truck. Since it's standard cab the GIANT F-150 Tcase (4406) won't fit. IT will be basically in the gas tank. You will have to use a BW1354M and get the adapter to use it on on the V8 tranny. A custom linkage will have to be made.
As far as the manual tranny you can go with the M5OD-R2. It's just like the R1 that is in Rangers except it's made for the 5.0 and the shifter is too far forward. You will need to fab up a custom linkage to make it work. Also a note, guys that have them on there big mudder F150s from the 90s have TONS of problems with it's poor design. It's internals can handle the V8 power but the aluminum case will warp and crack. Your engine power will be limited by the weak transmission. It's can't handle the torque. You may have to go with a automatic with a manual t-case.
I got all this info from Bob when I was researching engine swaps. Let me know when you do the swap. I want a 4.0 :)