A couple of things:
1. Position the cross bars so the canoe center of gravity (center thwart) is close to center between the bars.
2. Another member installed aluminum strips (2 in wide?) across the roof and bent down on both sides where the strip was attached to the side wall of the pop up roof. The cross bar towers were attached on top of each aluminum strip.
No holes through the roof top and weight distributed across the roof. I would probably add a center strip to stiffen the two cross strips and resist any torque from the cross bar towers.
3. Consider the Yakima system with a boat loader to assist with mounting the canoe from the side, or
4. Consider an additional cross bar at the back edge of the roof with a PVC pipe for a roller. You can rig a small winch (or two) to roll the canoe on and off from the back.
5. Check to see if you need heavier torsion bars for the roof lift system due to the added weight.
HTH
