Finally managed to find my OS 3.9 CD, this is the correct one.
So I formatted the harddrive, installed 3.1 but then it crashes. When I remove the startup-sequence lines about addbuffers on df0: and failat 21 and the other line then it boots fine.
So I installed IDEFix, it also works fine.
Booted up, loaded the installation of OS 3.9 and made the Emergency disk.
When I boot the Emergency disk it crashes (black screen, stops loading, after a while a guru appears).
So then I decided to install 3.9 from the cd while in 3.1, but the same result: booting lets it crash. Booting with no startup-sequence does work, but it can't find certain libraries (like workbech v44) to startup certain tools (like amidock).
Is this because of all the stuff that's in the Amiga and has no drivers installed yet?
There is a Cyberstorm + CyberSCSI MKII installed with an 68060, Multifacecard III, Ariadne II, Cybervision64 and a whole lot of memory (about 8mb or 16mb on the motherboard itself in 1 module and 128mb on the Cyberstorm).
Any ideas?