Stupid parts question, but...
So it's the side with the new caliper that doesn't want to fit over the new rotor, with the new pads installed?
(Might be a case of tolerances stacking up against you)
might be time to do a visual comparison
one more thing...are you sliding the caliper on from the top, or do you have one bolt installed and are "hinging" it in?
i have worked on vehicles where you can NOT hinge it in (dont think you would with a new caliper, but who knows)