Wilwood front brakes issues

Hey guys,
About three years ago I got a full front disk brake setup for my 1967 Dart GT convertible from wilwood disk brakes. The brakes work relatively well when they decide to work, but that's only about 3/4 of the time. I'm used to the pressure needed for manual brakes at this point, as I've been driving the car for the past three years, however some problems have begun to arise as I drive the car more to the point that I'm going to have to rebuild the whole system. I didn't have the instructions when I built the brakes, which was alright since my buddy is pretty good with disk brakes and he put together one side and I did the other. But apparently I didn't tighten one of the bracket bolts down all the way and it backed itself out into the rotor, which ate the whole bolt away, bent the caliper bracket and shaved a pretty sizeable chunk out of the face of the caliper. The caliper is fine in my opinion since the metal that was shaved away was just the meat of the caliper, and it didn't get to any of the actual parts inside, but I did have to replace the bracket, rotor, and all of the hardware. This time I made sure it was torqued down really hard and locktighted as well as the other side. That's not the problem that I have thought. The problem is that the caliper does not sit on the rotor so that the face sits flush or behind the wheel mounting surface. I'm pretty sure that this has to do with the way I spaced out the shims on the bracket, but I have been having the problem for three years now and it's starting to get a little impossible to find wheels that will fit with the way the caliper sits. I'm going to take both sides apart and rebuild them to see if following the directions helps :evil3: My question is if anyone has had a problem like this on their a-body with any brakes, especially wilwoods. Thanks for the responses, and sorry for the long post.