Not megasquirt i know but when i had mine converted to efi OFAB I used the engine loom connecter from the frst.
I used both male and female connecters to keep the engine loom seperate from the car loom.
It was just a case of isolating the mfi engine loom section, cutting it out and then soldering in the new connecters with the right feeds etc.
doing it that way kept it tidy and means if i want to swap to MS or any other ecu/engine setup it shouldn't be hard as i just unplug the whole engine loom