Your pages would load much faster and your logs/stats would be much more useful if you corrected the on-page links and includes, and implemented an internal rewrite from these new static URLs to your dynamic script(s). This is because a 301 involves the client (e.g. browser or robot) having to respond to the server's 301 response by issuing a second new HTTP request using the URL provided by the server's 301 redirect response; In simple terms, any page whose URL results in a 301 must be requested twice.
You are also relying on the search engines to properly ascribe the PageRank/Link-popularity of each 301'd URL to the 301 target URL. So, you've introduced a dependency of your site on the search engines to 'always get it right' -- Something we know is not always done perfectly.
Essentially, redirecting from a dynamic to a static URL is utterly 'backwards' from the correct solution, unless done as a final (and optional) clean-up step of the correct method.