LOL You are doing the exact same thing I just did to my A4000D :-D I also have the Cyberstorm PPC, so what you need to do is first of all DO you have an old A3640 card that came with the Amiga? if so then install it into where the Cyberstorm is as this is the easyest way.
Then install the OS3.1 from the install disks after formating the drive using the workbench disk. Install your CD drivers after that and then start the OS3.5 update as this will then install the O6O libs for your Cyberstorm. once you have the fullupdate installed then you can swap out the A3640 card again with the Cyberstorm.
Hope this helps.