There's a good and easy solution roll. Start off with a piece you can buy over the parts counter. It's HD part number 70264-94A . That's an accessory Y connector. With that you've got all the ends of the 4 pin connector accessory you're mating to up under the seat.
Take that newly purchased accy Y connector, cut off one male and one female end, splice an appropriate length of wire in between each leg, cover the hole thing with heat shrink, and you've made the perfect harness.
On mine I ran it from the accy connector under the seat through a frame hole then along the left side of the battery, then cross behind the battery to the right side of the bike, down underneath the strut and eventually tied off in a drip loop to the air shock fitting bracket. Some evenly spaced wire ties hold the harness to the bottom and back side of the strut. With the exception of the connector in the back you can't see the harness at all.
On the King tour pak that came to me without any holes in it I dropped it's harness out the right side. On the chopped I used the existing hole on the left side and then just tied the harness to the top side of the mount plate of the detachable rack. I wanted the connectors interfacing the bike and tour paks on the right side (the high side) just because they'll be easier to get to.
What you want to do can certainly be done. It's easy. It's the way Harley should have supplied a harness to do it to begin with. You just need to pick up that Y adaptor and you'll have all the spare parts you need.