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The long block should be a direct replacement, as long as you're using the '92 manifolds, wiring, & computer.
To go to manual, you'll need the aluminum pedal bracket, a new ($17@Ford) upper steering column shroud (for when you remove the shifter), a hydraulic clutch system (don't mix parts), flywheel & clutch, & crossmember. Also, you'll have to have your driveshafts cut for length. Go to http://www.broncodata.com/ and contact the webmaster - he recently swapped his E4OD for an M5OD in a '93 Bronco.