IF you have two people lining up an engine and tranny, it's easy as pie. I've had to do this a few times, and that's the way i would to it. I'd think lining up the mounts after re-installing the trans/engine would be more of a pain that just dropping the engine in and jiggling it till it falls together. I've never had any problems getting in an engine just by itself.
It really helps when you have a jack under the trans bellhousing and a leveler on the engine hoist chain, those are worth their weight in gold when installing an engine.
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem 
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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