I would suggest you remove motors as whole assemblies
Would that include the transmission too?

As far as the wiring harness goes I've removed most of the connectors on top of the intake manifold. Do I remove the harness connectors under the engine and leave the harness with the body of the car or do I disconnect it from behind the battery?

The motor that will go in wagon had head gasket replaced at 101K miles and waterpump at 81K miles, motor now has 135K miles so I should be ok with that. It also has a new mercedes a/c compressor installed just a few years ago.