As hinted at above, changing the case will be SUPER EXPENSIVE because of the injection moulding tooling costs. Just leaving out the floppy drive (or perhaps replacing it with a CF card reader in the same slot) would be much easier. Note that floppy drives are only a few $ each, so it isn't really a big deal for the price. And as Deft has mentioned, while we will be making MEGA65s the way that we think that they should be, you are all free to take, use and adapt what we are creating, and that this just adds to the community.
Paul.