I recently had my 10' kayak in the back of my truck while towing our TT. Tailgate was up and it gave me about a foot of clearance. Did a quick jack knife test before I left the house and didn't see a problem.
Set up is not ideal and is kind of a pain if you want to haul any thing else in the bed. Will be looking into a roof rack for my truck to make life easier.
As far as the kayaks them selves. What is the purpose of getting here a shorty? We have found that length is not much of an issue. But width can greatly increase stability.