Bolts collide with the backing plate

The bolts and nuts should be lower on the backing plate so they fit into the  depression in the backing plate.  (about a 1/2 inch or more lower)  The bolts and nuts stop the backing plate to seat.  Sure I could cut the bolt to make it shorter it will just fit a bit   (still tight and too few theads engaged) BUT:  The nuts will also not work in this position.

The red thing is a flashlight to help iluminate the problem.

When I tried to install the brake backing plate onto the pivot box it would not seat in any way.   The lower bolts, when fastened with lock washers and nuts will not allow the backing plate to seat.   I think the position of these holes and the cross support is at least 1/2 inch too high in the box. ( and the box should be that much longer too)  But this what I have.   Anyone else have the same problem?  What did you do to alieviate it?  Will my changes work?   Is there a more elegant way?