That's what I did at forst too, copy everything straight from WinUAE.... errors galore, you know how I ended up? Installing all from scratch, fresh fresh, on my own. Now I have a very nice WB setup
I recommend you reinstalling everything from scratch. It will be worth all teh time spent on it
I'm yet to try a CDFS... I installed CacheCDFS but havent tried it yet, I need to make a cable long enough to reach out to the CDROM from inside the Amiga case into the PC case