After installing modular X there was one problem: There were two paths in my xorg.conf that pointed to the old /usr/X11 places. Those where ModulePath and RgbPath. I changed them like this: RgbPath "/usr/share/X11/rgb" ModulePath "/usr/lib/xorg/modules" It seems that RgbPath also doesn't exist, but the x server doesn't seem to need it.
Neither of them need to be in the config file, you can just remove both lines. Our config tools are being updated to not put these in the file anymore. I've updated the X server %pre script, to remove the RgbPath line, and to check for ModulePath, and if the old X server module path is defined, to switch it to the new path. Fixed in: xorg-x11-server-0.99.3-6