The 01 F250 that my wife drives has done the same thing. (It's a 6 spd). You'll just be driving along and lose all power: runs, idles fine but NO acceleration. Usually stop, kill and restart truck and it's fine. It used to do it pretty often but after I replaced a bad CPS it quit for several months but it just did it again the other day.
And this may sound strange but when i used to drive it everyday(instead of the wife) 90% of the times it did this was after I cut it off/back on to order at the drive @ lunch.