Motor mount problems
 

I had a 1997 502 Gen 6 block in my boat, mounted to the stringer angles with Gil offshore mounts. Recently I had a new engine built with a new Gen 5 Chevy bowtie block. I installed the old motor mounts to the new engine but while installing it in the boat the existing holes on the stringer angle irons do not line up. I bought new aluminum angle irons and drlled new holes that had to be drilled 1/2" lower which raised the motor 1/2" so that the alignment tool would go in. Now I go to install the tailpipe sections of the CMI headers and they dont line up. I was just curious if anyone knows if the bowtie block is drilled differently to cause this problem. Thanks for any input.