Unless you *really* need SSI's, you may want to consider getting the functionality of SSI from Perl. Pretty much all of SSI's functionality (well, as much as I can remember, it's been years since I've used them) can be duplicated by Perl. Most of what you need is probably in HTML::Template (ie. this will allow you to include files, so you can have your layout in separate files, and won't have to update every file when you make layout changes.)

SSI's can be useful if you don't have full control of the server, and your admin won't let you install much, but it sounds like you have access to your server, so you can install stuff off CPAN.