Novice wiring questions

"strip only."

I would NOT use a factory harness and I would NOT use a bulkhead connector

Buy yourself a universal xx circuit (12, etc take your pick) harness and go to work. Install an underhood relay/ fuse/ breaker panel to pull heavy loads like ignition/ charging, pump(s), fan(s), etc.

You can either use the old stripped bulkhead connector to feed wires straight through, or just make a little aluminum cover plate with a nice big grommet in the middle.