I think nspctr1 has a good idea with the front and back supports.
I don't agree that no stress on the windshield is good. The W/S is supposed to be supported up top, with the top. With nothing holding the W/S it will flop back and forth over time, I've seen them snap the hinge bolts (no fun on the freeway). Anything tied over the top will help secure the W/S, but not real well since there isn't much to tie it too. Not having the top on for extended periods can also stress the center of the frame, so I'm told, but I've never seen an FJ40 frame taco'd.
Ideally, if you travel most of the time w/o top, you will have rubber mounts that tie the W/S to your front cage, which also, btw, supports the canoe/kayak.
Paul