So this is not my first craft build, and basically, it's identical to my last setup on the craft front, I can't see anything wrong, but I can't remove index.php without causing a 404. I've tried the .htaccess fix, not luck. The last site I did simply had "deny from all" in .htaccess, but it didn't need index.php, so I don't see why I would need to change that for it to work? Is there anywhere else I can look for a settings change that might allow for cleaning up the urls?
Check and make sure your .htaccess file is in your public HTML folder
If you do not include your .htaccess file in your public folder, Craft will display your home page properly, but all other pages will fail to load unless you add
index.php?p= in your URL.
http://website.com/mypagethatreallyexists = 404
http://website.com/index.php?p=mypagethatreallyexists = Your page
http://website.com/mypagethatreallyexists = Your page
omitScriptNameInUrls to true in your