i did this upgrade a few days ago.
start off by putting the new mamewah in a different directory and copy over stuff one at a time.
I was able to copy over my files directory, and my layouts directory.
I copied over my ini directory but then I had to go grab a newer version for the ones that don't have a number in them. so mame.ini needed updating but not mame-0.ini. You can find already configured ini files here for all sorts of emulators:
http://home.comcast.net/~cpviewer/downloads.htmMake sure to fix the file paths and screensaver settings and what not.
mamewah.ini will need updating too. But most of these updates are pretty easy to copy and paste your old settings into the new files.
Once I updated the ini files all my old lists worked great without needing to be regenerated.
Joseph Elwell.