I was able to push the upper bolt all the way in, at least as far as I can see. I am not using lugnuts to hold the rotor back.
The problem seems to be on the outer pads. Actually, I need the caliper to be pushed out towards the center of the vehicle but the outer pads are in the way. If I fit the caliper over the outer pads, then I cannot fit the lower part of the caliper. Seems like I need to do something to push the rotor further into the vehicle to get the clearance.