I carry three 'yaks, including one 14' hull, on a triple-wide Thule rack mounted on my crew-cab roof. Plenty of clearance between the 'yaks and the TT. Unfortunately, it doesn't meet one of your criteria - cheap.... The Thule systems are a bit expensive, but given the cost of decent kayaks, I view a good, secure travel rack as kayak insurance.
2014 RAM 2500 Laramie 4x4 Quad Cab w/Cummins Turbo Diesel, 2009 Rockwood 2607, and 3 'yaks!
300W of Suntech Solar, a Rogue MPT-3024 Controller, and a Xantrex PW2000 Inverter