Excellent. This might be a stupid question, but I can update one partition to PFS, test it out, then do the others right?
That way I can do backups etc, a bit at a time.
Yes, given that PFS3 will fit on your RDB. Try and add it with any filesystems you already have installed, then you'll see.
And what I am wondering, is if I could take an 8Gb CF card, plug it into my MorphOS machine, partition it and format it with this file system, then plug it into my Amiga 1200 or what ever, and be able to do a WorkBench 3.1 install onto it.
Yes.
Or, would I need to make a custom boot disk for my Amiga, then do the dirty work from there?
That is also a possibility, but MOS should do fine.