What I would do is make a WB partion on an old IDE drive that is not going to break the 4 Gig barrier. They are very easy to find and often very cheap. Boot up on it as master set the boot prirority to 3 or something using hdtoolbox. No go fiddle installing CDFS or some other CD driver, even get one from the AMinet or use a disk filesystem like PFS3 which by the way, I think is just the cream of creams, it fully supports big drives, just load it into the RDB Rigid Disk Block again using hdtoolbox and make the drive bootable.
Once the large disk is recognised, just do a strait copy of youw Workbench drive over to the big disk and away you go.
I had the same problem as you except I had only SCSI drives and no IDE. Try doing that on a fastlanez3 SCSI!! You can't load setpatch or any other sys drivers as they patch the scsi.device and Fastlane won't see anything!, My CD rom was SCSi also, but as you guessed, doing what I mentioned above soon got me going and I then upgraded to OS3.9
There is another way... if you can make a bootdisk that patches the SCSI.device for your IDE drives TD64 or something, you could then do all this without the need for finding a small drive. Anyway, there's a few things for you to try.
