I never use the brake levers to clamp down and tighten things up, which in my 12 years in bike shops, never worked for me. Last time I did this was with BB7's, and even in that instant I used business cards between the pads and rotor, which helped, but ultimately tightening down each caliper bolt a little at a time is the best way to get everything aligned. OP did the correct way of centering brake calipers.