Have you made a lot of changes on the pages? It may be easier to revert back to the original files if you have not made many changes to the pages.
Can you link me to a site where the store is hosted?
Also, in your WA_Globals.php file, what are the values of $WAGLOBAL_Root_URL, $WAGLOBAL_localRoot, and $WAGLOBAL_remoteRoot when hosted on the remote server?
As for the AssumedRoot issue, I'm not sure why you want to remove this. Is there a reason for that?