Sorry I didn't read the whole thread, so I might repeat some stuff, but it should be simple. 1st you don't need the 3.1 disks for your CDRom to be recognized, just install a cdrom filesystem that's AOS2.1 compatible. I suggest IDE fix wich also might solve a few problems of the IDE bus.
That's it!
As for CD0 driver from AOS3.1 not recognizing your CDRom, it can happend because of incompatibilities with the Amiga IDE's port and the CDRom (again IDEFix will fix this), or simply it's set to a unit/device that doesn't correspond to your CDRom. Open CD0 in a text editor and edit the device and unit to match your CDRom. If this fails, get IDEFix (your need to configure it too, of course).