Unless you remove the tranny first(pointless when you're removing the engine too-No offence Tekkie
) drop the engine through the bottom.
One more recommendation:
Only remove portions of the harness connected to the chassis. Removing the harness from hard to reach sensors sucks when the engine is still in the car. There are a few connectors on the left side of the bay by the alternator, the PS connector on the rack, the power harness from the + battery terminal, the ECU plug and, the dash connector. Lower the engine slowly, stopping every few inches to make sure you got everything. Once the engine is low enough pull the ECU and dash plug through the firewall. Once it is out simply transfer the harness to the other engine. It really is much easier this way. I don't know why this hasn't caught on...
good luck