[eluser]BrianDHall[/eluser]
If it can find the default controller but nothing else, then to me that sounds like routes is the next place to look. You could possibly have a route defined that is grabbing more than you expect and sending it places you don't want it to go.
So check and/or post the routes you have defined, and then check your project and be careful of any use of remap() functionality, very easy to throw 404s if you aren't careful with those.
Also I'd go ahead and delete .htaccess from the server and change your config file to use index.php. This narrows down what could be going wrong so it should be easier to get it working and then work your way back to removing the index file.
