Hy/Rd first impression: first, I found them difficult to align without rubbing the rotor but attainable.
Are you using compressionless brake housing? That gave me some trouble on the Chinabomb due to its stiffness and the short run of housing between the internal frame routing exit points and calipers. I had to unseat the housing from the calipers in order to get them to self-align with the pads engaged (actuating the brake arm on the caliper by hand). With the housing installed in the caliper stop, I think the stiffness of the housing was high enough to flex the rotor slightly resulting in imperfect alignment after tightening the fasteners no matter how many times I tried.