For starters, I know nothing about the se.nsuo.us cleanurls addon.
If that addon already gives you the URLs you want, then use those URLs instead. Don't install the modified pagedarchive.php included in the template and then edit ~4 HTML files in the template so that ANY URL in the template uses the se.nsuo.us cleanurls instead of 35mm URLs. Its not hard. Manually search and replace for any URL.
What else can I tell you. These are all giant hacks to Pixelpost, since it just was not designed around clean URLs.