I found it pretty straight forward.
Unwrap the whole engine bay loom, using cable ties as you go (to keep the shape and branch lengths), then cut off the two ecu connectors, then pull the wires out.
A lot of the wires loop the two ecu's together, some go back to the fuse box and the others go to the two relays under the dash (ignition and fuel?).
Work on the basis that you don't need any wires from the ecu's. I also removed my fan wiring as my megasquirt is going to control my fans.
Then when all the ecu wiring is out the way and everything is insulated properly, shove the battery back in and test your lights etc, if its all okay then re wrap your loom.
Job jobbed.
Rob,