1. ......I don't know if the proper fix is to just apply more coats of the same finish over top the original finish. Or if the whole thing needs re-skinned. It may even be fine to continue using as is. What would be the best way to proceed with this boat?

You didn't say what you coated it in, but if the skin is not damaged AND the finish is not flaking off, just recoat it. The coating is your waterproofing and I have had to repaint a couple that started to seep water through a bad scratch.

2. ......I have a factory roof rack on my Subaru, and J hooks to hold the boat. Would this be safe enough to haul for that kind of distance? Is there a certain speed I should stay below?

Tie the straps to the factory rack, not the add-ons. That way if the cradles fail or come loose you are much less likely to loose the boat. Flying boats are deadly to those around you.
Consider two straps on each end. While rare, straps do fail.
Put on at least a bow line and maybe a stern line. Bow line is law is some states but it is just a darn good idea to keep you out of trouble. Just make sure it is securely attached to the boat.
Do all that and don't worry.