Hi Steve
When i was a final year student at university there was a project for floppy and hard disk controllers, I tried to take it but the supervisor refused to give it to me.
In anger I went and bought myself a 3" floppy drive and asked the manufacturer for a datasheet for it. They mailed it to me for free ( emails were not very popular in the 80s) and after reading it I found that it is very complex to control it on your own, so I bought the FDC765 single chip floppy drive controller chip and I interfaced it to the z80 which was popular at the time.
I Cant remember any more details because this was in 1987 and I was very proud of myself making my own first home made project. Kept on braging about it to my postgraduate students (friends) at the university for a long time. Retreiving and sending the data to a floppy is not a simple task that a microcontroller can handle, you need phase looked loops and frequency modulation ... etc. So why re-invent the wheel, get yourself a single chip solution and interface it to the disk drive.
The question about file systems and FAT is a completely different storey and needs a project on its own.
Unfortunately few years ago I searched for the datasheet of the floppy disk drive but must have been lost while I was moving house.
So I suggest you look for a datasheet for a floppy disk drive, it will explain to you exactly how to interface it and you would appreciate the creaters of the single chip FDC chip.
Also a datasheet for the FDC765 ( not sure if it is the right part number) will teach you all the basics of floppy disk interfacing
good luck
Regards
Mahmood