what you really need is a set of working workbench floppies. and do a fresh install of workbench. you don't need 3.1 rom for writing adf's to disks. but transferring those adf's from PC to amiga will be a problem. you can format a 1.44 floppy at PC (normal PC format) and use it on amiga with crossdos. It should read 1.44 as a4000 drives should be HD. you can transfer one adf at a time this way (880 k)
as for your question about the cd rom, I think 3.1 workbench had some cd rom support albeit very buggy. You need a cd rom filesystem, what was it I used ... amicdfs ?
