Need some ID's

I want to keep the interior vent system that hangs below the dash. I also want to remove any wiring for air conditioning. Can I just dead head it at the bulk head connector ? I also want to remove any of the old electronic ignition, and emissions. Can I just dead head those at the bulk head ? But I want to reuse wiring for the charging/alternator because the new alternator will be positioned in the same spot, using the same type of voltage regulator.
When you cut a wire at the bulk head are you creating future problems with corrosion in the plug ? is there a proper way to remove wiring ? That's what I really need the help with. If I know which items do what, I can discard them, if I need to.
When we get off the subject it gets confusing. I have a lot of the old stuff that works with my engine, and the red ignition box is getting installed under the dash for neatness. I really want a sanitary install. You pop the hood there's nothing excessive that you see.
My wife doesn't make me sleep in cars, or on couches, she sneaks up on you in an electric wheel chair, and barrels you over. Actually you should see what happens at the mall when they violate code by shoving racks in the isles. BOOM.