bbt,I wouldn't move the wings back,don't want a short coupled plane.On the incedences,you might want to add around one degree of positive to the stab,lotta biplanes need that,even the Ultimate.You don't need to make a copy in CDR for me,i can open DXF etc.
Not to sure about the 2 degrees of downthrust on the engine,if it was me i would set everything at zero except for two degrees right engine thrust,one degree positive on the stab.Then build the plane and make adjustments as needed,might even want to consider lowering the top wing a bit and see if that smooths things out any.Pretty darn cool plane,well worth taking the time to experiment with the settings to have a superb flyer.