I had already modified the .htaccess with the re-write rules. The permalinks are written as desired, but the pages cannot be found at the new permalinks.
To clear things up, it’s just the base name of the URI that I’m having problems with. For example http://ilaughdev/laughjournal/index.php/author/jon/ still works (after I had removed index.php from the blog URI), while http://ilaughdev/laughjournal/author/jon/ is the link generated on the page (which is what I want), but the page does not exist at that location.
That is, the actual page still resides at the URL with the ‘index.php’ in the name instead of the new URL that I’m pointed to.