I'm not gonna write regex here, but I'll give my .02. Create a script that opens a file, runs some regex's over it and spit it out to a different file (in case we break something)
If it starts with #!, leave it alone. If the line starts with a #, its a comment so delete it. If you find a # elsewhere, and is preceded by a ; (possibly with whitespace in between), hack off the end of the line. That should take care of 99% of your problems.
I'd write it up, but I'm not at home now and don't have access to perl to test, so I won't confuse with bad code. Maybe I'll drop back in and write it tomorrow though....
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