Take those extra connectors in the first pic and cut them out of your harness as far back as you can, and then tape it back up.
Is it just me, or does it look like the front of the intake seal is pushing out in that third picture?
Those seals are a joke, and like to blow out. You're better off running a bead of RTV across there instead of using those shitty rubber things.
Not sure if the V6 cars had these, but there should be a metal collar that protects the starter wires.