I think that you can just change the hdfs on your winuae install, then make the shell replacement and you should'n get any problem. I never used shell replacement and don't know the details about it, but i suppose it simply replaces the commands with winuae.
On another note, why are you using a competition pro for joystick?. My hands hurt even thinking about it, and i would go for a arcade stick or gamepad, but if you like it, then it's your choice.
Is changing the shell doing anything more to the xp installation?. Is the xp system still underneath it(i think so, in order to be able to boot), but as i said, never got the chance to play with that feature. What are the advantages of the shell replacement?.
