My experience is with an auto tranny so not sure if it will be the same but I can answer a few of your questions. If you disconnect the ECM and unplug the connector to the firewall on the drivers side, then with a little bit of work you can remove the engine wiring harness to include ECM connector, Passenger side fuse block, headlight connectors, and maybe a few others I'm missing right now all the way around to the connector on the drivers side firewall. The wiring harness on the engine for the sensors and injectors are all going to a couple of plugs that unplug from the main harness. You will also want to be sure to unplug the 02 sensor. I pulled my motor and tranny out together after removing the radiator and disconnecting the cat. converter. A lot easier than dropping the tranny and removing the engine.
So now the only question is will your manual tranny from the 2.9 work on the 4.0
With the automatics they will both bolt up, but the 4.0 tranny has the parts to handle the extra torque. Not sure of the case with the manual transmissions.
