If you're not doing anything to the transmission I'd leave it in and just place either a good floor jack or big blocks of wood underneath the bell housing to keep it level in place, that's what I did.
DO NOT REMOVE THE TRANSMISSION DIPSTICK TUBE...lol lol...otherwise tranny fluid will piss all over the floor AND you'll have to replace the dipstick tube O rings.
Unbolt the transmission from the back of the engine and when putting them back in "hand thread" them all they way FIRST so there's no chance youll strip one. Don't forget to unbolt the 4 torque convertor bolts and DO NOT PUT THE TQ NUTS BACK UNTIL THE ENGINE IS FULLY BACK IN AND RESTING/BOLTED to THE MOTOR MOUNTS otherwise you could pull the TQ forward and tranny fluid will leak out from the seal there.
I removed the upper fuel injection plenum so I wouldn't have to take off the hood to pull out the engine as I was by myself with a rented engine hoist but it was no problem but the only thing you need to get a feel for is how much chain length you need with the hosit to lift the engine up, over the radiator core support and set down then repeat with the new engine going in.
I had a chain across the top of the engine using bolt holes front and back, left/right side so if you do it that way the engine wants to turn either coming out or going in so it might better to bolt in the center where the FI plenum runner is located on the lower intake manifold BECAREFULL and make sure the manifold bolts are secure/tight to handle the weight there.
If you remove the upper FI plenum you can leave the EGR valve on along with the throttle body disconnected etc. but you should dissconnect the ERG tube and then remove it from the lower intake manifold so it doesn't get damage or cracked, they're expensive and can be difficult to find and you're porbaly going to repaint so parts need to come off anyway...NBD
The other thing I did was use blue painters tape and labeled vacuum hoses and every m/f sensor harenss connector so when reconnecting it was a no brainer where everything went. I also took some time and visually inspected the harness for damage, chaffing or bare spots and using CRC Electrical spray cleaner where it just evaporates then retapped those questionable spots where the tape was dry/brittle etc. etc. while working with the engine out/in I layed the harness off to the drivers side out of harms way just in case.
You'll notice that some elec. connectors can be disassembled where the us-snap and come apart should any be broken or cracked etc. RJM/Ford Fuelinjection has a wide variety or pigtails are available in most auto stores not expensive.
I found plastic freezer sandwhich bags you can write on extremely helpful for inventory and grouped parts and bolts together on the garage floor like an assembly line to keep track and a wire wheel brings back a lot of parts and bolts for cleaning and repainting parts.
Make sure you know How To "stab" a distributor and don't forget to "manually prime" the internal oil pump before you bolt it on with the oil tube and screen the oil pan. Prime the oil galley around the push rod and lifter areas with the lower intake manifold off and then using a drill and special "priming tool" attached to the oil pump shaft run the drill with priming tool for 5 miuntes circulating the oil all around inside so when you fire up the engine for the first time everything's lubricated, lifter setc. etc. you know....
The "priming tool" costs $35.00 now sitting in the tool box until I die before I'll use it again I'm sure....lol lol
Take your time and work thru it slowly depending on what length you're going to with the engine...
www.supermotors.net/17406 - engine swap dtd Aug/Sept. 2008 and you can see what I did for reference.
Just a few thoughts!
Good Luck ~ :thumbup