please take a few pictures of your cable setup (especially from the cable stops on the down tube and under the BB shell). This may help in the diagnosis of your issues. Otherwise, you should just bring it to a shop and show you how to fix it (a GOOD mechanic, not a shop like Performance or something)

I have dura ace 7700, with standard jagwire cables and housing, and I have very little friction. New DA with nokon should have almost no friction (though there will always be some that you will feel, unless you get DI2 which you wouldn't feel the friction through your hand).