Try the tool on Aminet: util/misc/MakeSuperDisk.lha
Short: V1.6, Makes SuperKickstart disks from ROM files
Author: Olaf `Olsen' Barthel
Type: util/misc
Perhaps whatever you were using to make SyperKickstart disks wasn't working, try this.
Also, you need to make sure the ROM you are writing to disk is the correct version for a A3000D, e.g. a A1200 Kickstart 3.1 ROM image won't do the trick IMHO.