Have to agree with what Rusty is saying here. The factory put in connectors, as they were building cars on an assembly line so they installed the wiring harness in sections.
A through hole in the firewall with a grommet is a great solution. Once all the wires are in place you can weather proof the through hole by injecting some RTV around the wire bundle.
If you ever needed to completely remove the harness, perhaps if the engine compartment was being repainted you could remove each wire / pin at the MS3 ECU connector and slide the wire bundle out of the grommet on the engine side of the firewall. When the harness is re installed you would certainly need to get each wire back in it’s original pin position. There is a diagram in the MS3 manual and each wire is numbered and color coded on the MS3 harness.
This solution also eliminates any voltage drop or water intrusion issues associated to a connector.
