Problem Default Dragonfly causes CTD

I can't help you with that because I've never used Dragonfly since Tranzit was released and I don't remember a thing about its overcomplicated control.
 
The Dragonfly doesn't adjust the COG, rather it adjusts the RCS to account for the COG being changed by a docked object. There is a limit as to how much the Dragonfly can adjust, however. This is especially significant during translation.

The technique is to use a "nudge" of Linear RCS (using the <ctrl> key to use 1/10th strength helps) then switch back to Rotation and fix the attitude.
 
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