The difference in compilation overhead between 200 lines and 400 lines is more than likely so negligable that you're probably barking up the wrong tree. If this is in a web context you'd probably get a much better boost by using something like mod_perl or FastCGI.
That aside, yes you probably should see if you can't break things out into smaller subs (at the least). It should be more maintainable in the long run.
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