Steve:
Forget it. You will be OLD before you get any kind of reasonable solution to operating a floppy disk drive without a controller. I spent quite a few years of my career making floppy disk controllers back in the days before LSI chips that did this and then afterwards as various LSIs came into vogue. You have to trust me that you are wasting your time trying to interface a floppy drive with software and a few flip-flops.

Why don't you consider interfacing a Compact Flash card to your microcontroller instead. It will work WAY better, is all straightforwrd logic, and there are sample ideas galore on the web if you search via Google.com. Particularly check out the Sandisk web site. These matchbook sized flash cards are way cool. You interface one of these to your microprocessor and you will have megabytes of storage available in a removable format at a quite attractive price.

Michael Karas