I have seen photos of some builders who suspend their kayaks by putting a 2 x 4 inside each of the hatches and attaching a rope that goes to a hook on the ceiling of their work space so they can varnish the hull and deck at the same time.  The 2 x 4 needs to be longer than the hatch opening so that when the rope is pulled the wood doesn't slip out of the hatch.  Or, if you don't have hatches but have drilled holes for carry toggles, I have also seen photos of builders who put a dowel through the holes and suspend the boat from those points.  

Either method allows the hull and deck to be worked on at the same time.  Or you could fashion some custom cradles that are a few inches shorter than the deck width.  I think that it will be a bit tricky to work on both sides at once.  Would it be possible to paint the hull up to the shear line, then after the paint dries flip the kayak and do the deck?  You might try this on a sample piece of wood to see how much of a line there is where the two surfaces meet.  This would allow you to do a more controlled job with the paint. 

Good luck and let us know how it worked out.  

I hung mine with wood in the hatches and straps. The issues I had was that it swung a bit and, until I bought more lights, it was hard so see well underneath. And kneeling on the concrete floor was not real comfortable. I think next time I will do the hull first, then flip it over and do the deck with the boat on horses or my bench