I can't get my disc brakes back together. Are these pads to blame?

[BrentBTK]

I am in the process of replacing control arms and spindles, and the rotors were shot so I'm replacing them and the pads as well. It's been a nonstop struggle. Multiple trips to the parts store, wrong bearings, missing seals, brake lines are too short now, all the problems. The one I can't figure out is getting these new pads loaded into the calipers and getting the calipers mounted. With the new pads in, I simply CAN NOT get the holes to line up for the caliper bolts. So, I started comparing pads, and I see 2 "rivets?" on the back of the new pad that are preventing it from sitting flush in the caliper. I tried filing the rivets down flush, and I'm definitely closer, I can get the bolt in the hole, but it's canted against the rotor. It seems like the caliper is just twisted a bit with the pad in. Is it these "premium" O'rielly Auto Parts pads? It's day 3 and I am beginning to lose my good humor Pics below of the pad and the bolts not lining up...