Pull carburetors, and either do a complete overhaul, or at the very least return them to stock configuration. Altering the Needle height with shims and orwasher's will directly affect the mixture. That is the one thing that was done that stands out in my mind as potentially being at the root of your issue. I have messed quite a bit with a needle height of the carburetors in my Valkyrie addressing fuel consumption issues and one Groove in the Dyna jet kit makes a difference of three to five miles per gallon.
Also, I don't recall seeing or hearing about your spark plugs and their condition. I would expect them to be dark, but that's a very simple confirmation that should be made.