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Out the bottom, and no, you don't have to pull the engine. You just have to get the truck up high enough to pull the tranny out the side. Linkages on the driver's side, electronics on the passenger side, driveshaft and crossmember in the rear, and bellhousing bolts in the front. You may have to undo your exhaust to some degree, too, to give you better access to some things.
Might check these links. The guys over at the FSB forum have done a couple of really good write-ups with pics on dropping an E4OD. Really helped me anywho.
Depending on what you use for a jack, you'll have to get it so it sits flat on the jack. Due to the E4OD's hump in the pan, you may have to get some short 2x4's and a strap to keep it steady.
Yeah, slap a wrench on the crank and turn it by hand. Make sure you know which way to turn it first (I don't remember offhand, I always have someone bump the starter while I watch).
Jason
On edit: by "wrench", I mean something long like a breaker bar with a socket. A 1/2"-drive ratchet should be enough.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.