Hey Phill, just looking over this and it seems like you are on the right track, but maybe through fiddling you have the links to the swash at the wrong length affecting everything from there up.

Time to start again me thinks. Navy blade on RC groups has been going through the similar problems and through some help form others got all the default factory link lengths. He has done a pic with the lengths on it they may help you out.

Start by setting all servos to mid alignment to their cases using subtrim, with pitch at 50% and all normal trims to 0, dual rates, expo etc all to stock default settings. Use a pitch curve of "stunt mode" with a little mod on the middle 3 points (ie, on a 5 point curve like the dx6i set the pitch curve to 0, 50, 50, 50, 100; center stick is not so critical then but you still have full throw top and bottom).

The swash to frame measurement is with the pitch at mid stick (50%).

This should be an excellent starting point, then you should be able to just adjust the links to the blades to fine tune 0 pitch at centre stick.