Ryan,,I'm assuming you're talking about the kind of suitcase handles that are on SeaLions/Eclipses? The srcrew in the ends could easily be secured with a #14 wood screw and finish washer into a 1oz end pour, for the inboard screw how about gluing a block of wood under the deck with some careful measuring? A little 1/16 hole and toothpick would bracket the forward placement of the block as you reach into the suspended kayak and plop the wood block in position with a generous dollop of thickened epoxy you'll have a solid piece of wood to drill into. What I did on the Merganser I made was cut a slot in the deck near the ends and dropped a 1 1/2" diameter ss. ring into the slot of the end pour and glue it into position an inch or two back from the ends,,that was the connection for the toggle but also to allow the kayak to roll/around without the wood getting bashed on top. Maybe those suitcase handles could do the same.
Another thing that is partially ergonomics and aesthetics is you can carve dow the straight entry a bit (1/4") to give a little nose and reduce the sharp edge right below the ends,,that makes the ends a little easier as a hand hold for a two person carry or when grabbing the end of the boat.