I suppose that your WarpEngine needs a special version of 68040.library and most if not all of your crashes are caused by using the Commodore version of the library. Or none at all.
Actually I wonder what makes you think that OS 3.9 could run well from harddisk when it fails to run from floppy/CD. "Installation" of OS 3.9 does nothing else but copy files from CD to harddisk. The same files which failed to run before.
