Voltage Regulator Question

I think I am going to upgrade to the later square back alternator. I have already purchased the alternator, voltage regulator and connector. The problem I am having is when I try to bolt on the new alternator it seems that my old brackets arent correct. The back of the alternator is practically touching my aluminum head and the bottom adjustment bracket doesnt line up with the bolt hole in the new alternator. Any guidance or help would be greatly appreciated. Thanks!