Have you created an emergency boot disk using your A3000 which includes the correct 68040 libs for your accelerator/cpu card?
Some things (libs, any rtg information, mountlists, etc) are copied from the emergency boot-disk as part of the installation process.
Could you be a bit more specific than "Problems galore"?
It's really a shame that we can't redistribute the contents of the Amiga OS 4.x boot floppies. They contain OS 3.x software intended to boot up the Amiga from the OS4.x CDs.
It is by far the smallest and most efficient way to get access to a CD-ROM on the Amiga (assuming you have one actually connected).
It even works if you have two drives on the stock IDE port of an A1200 with no other hardware.
The process goes something like this,
It first kicks version 52 of the scsi.device into memory and reboots
It then runs the tool c:CDMounter which uses l:BootCDFileSystem and possibly devs:ATAPIismajik.
It's like 3 files, no mountlists and you get large HDD support. It's pretty amazing.