My Jon does not have a deck, so I'm literally standing at same level as the water.  I've found pitchin/flippin with a 6.5' or 7' rod is pretty much impossible.  The rod is so long I can't get the good pendulum swing like you need because the rod tip hits the water.  I'm thinking about trying a 5'5 rod.  Anyone have tips for jon boat pitchin/flippin?

stand on the seat if your boat is stable enough

if you don't elevate yourself its tough

I find that on the down swing my jig hits the boat

That is an awful short rod for flipping and pitching.  I do not feel like you could get the leverage needed to get the fish out of the places you are flipping and pitching to.

Short, easy roll casts are just as effective if the area is accommodating enough.  When I am fishing from a Jon I find myself fishing this way when targeting specific pieces of cover.  

I am sure more experienced Jon boat fisherman will be along shortly.  Perhaps they can give you some tips and techniques I am unaware of.