Need help perfecting the budget build hemi swap

The next big thing, is wiring. Since I'm removing everything from one car, and installing it to another, I left all the components attached.
One thought is, it would be quicker to wire the engine compartment, and than unplug the MSD hemi 6 box. Than find a way to feed the 3.5" by 3/4" inch plug through the firewall. Thus the box could be mounted in the interior of the car. Since I have no intent on having air conditioning, I though I might feed the plug through where the air conditioning plumbing enters the interior.
On my 69 Barracuda the heater core tubes come through two round holes in a rectangular plate screwed to the firewall. I'm hoping that the air conditioning tubes mount similarly. I don't want to cut things, if I don't have to. The reverse way would mean feeding out several plugs with the labels I marked them with.
In this area, I'm up for lots of suggestions.

Any particular reason you're running the MSD box inside the car? Aesthetically speaking I agree that it would look much nicer (especially with all the extra length they give you in the harness), but it's a weather sealed box, so you can run it in the bay. I had the same quandry when I built my car. I really don't care for the big loop of wiring I have to take up the slack, but it was the least painful option as opposed to figuring out how to get something through the firewall. I've had my box on the inner fender for a few years now with no ill effects.