Don't edit perl's syntax highlighting, edit your colorscheme. The idea of syntax highlighting is that the syntax highlighting file simply identifies functions as functions, comments as comments, etc, and then your colorscheme file matches up colors to those things. A syntax file should not have any references to definite colors.
Beyond that, I can't really say anything. I don't know what color file you're using, so I don't know what you'd have to edit to change the colors to how you want them.