I went with a BW 4406 manual shift out of a 2000ish F150. I used factory driveshafts, front is from a 97 F150 4.6L, and the rear is out of a 5.4L Expedition. Kinda funny how that worked out to not need custom shafts.
It was the same bolt pattern, and with a little bit of coercing with the sledge (clearance the floor pan, but only a little) it bolted right up. No need to clock, it tucked up in there nicely. I needed to use a conversion u joint on the front shaft at the differential end. The manual fits better than the automatic, as the shift motor would interfere with the gas tank.