So I reinstalled 3.1 *again* with the 68060 and 68040 libraries and made a new Emergency disk. Now everything worked fine, also stuff from the OS 3.9 CD that didn't work before.
So I went on to install the Cybergraphics drivers, fine too (nice sharp image at 800x600) but when I boot from the Emegency disk, double click on the Amiga OS 3.9 CD, double click on the folder which contains the installer and then it crashes: everything hangs. Even the mouse doesn't respond.
Maybe the video drivers?