Sort of. If you already have the manual gearbox in and working with the auto ecu then you can swap ecu's as much as you like. Its when the 5 speed conversion gets done that the looms are swapped.
This is the auto loom
These two plugs connect to the loom at the back of the engine
The manual loom is much simpler and only uses the one rectangular connector
so the round plug (that connects to the solenoids in the auto box) dont get used
If you plug the loom in as is, it will work but you will be able to start the car in gear. If you swap two pins over (cant remember which ones) the ecu wont engage the starter motor unless the gearbox is out of gear.