I think what Bill is saying is you need to hog-out the mounting holes in the bracket that attaches at the points in the picture...
I had to hog-out the holes where my bag brackets mounted to the frame to bring the bags down, mounting holes in the fiberglass fender to bring the fender up, and get rid of the rubber mounts between the bag and the bag bracket... and it still didn't line up perfectly.
Pro Tip: I don't recommend attempting to lower the bag brackets because now my rear swing arm hits the mount when I bottom-out.
Not only did I have to slot the bolt holes as mentioned here but I also shimmed out the upper left rear saddlebag bracket and rebent the right one to make it shorter. Its a common problem but when you do it right the results are well worth it. Few things get me going more than seeing a top notch bagger in a magazine with a 7k(+) paint job but lousy fitting bags and fender.