Well, Thomas will most likely be the best to consult on this one, as he has a lot of the same hardware as you do, and I don't bother setting up my Fast ATA for the A1200.
If you erase all the .prefs files, the only thing that will be done, is that all your changes on the workbench will be erased. You don't need to install any files afterwards, just open all the prefs tools you need, and save the changes to the the settings that you like.
If you wan't to see which files the CDFS install program copies, then select to have a log file. Then you can track the files from the install script, and manually owerwrite the needed files afterwards, if the script copies an older file than the one on your harddrive.