Dave, i used to have a yakima rack on another truck topper and it had the vertical bars that held the kayaks on their sides. could you put a post in the middle of the spare and a vertical post on the front bar? you'd have to jack the height up in the front so the nose of the kayak doesn't hang down in front of you while driving. i know what your saying though about it being a PITA to load. it was easier to do with 2 people, but still sucked.
here's a quick, poorly drawn pic of what i was saying.