I bought an old floppy drive from a local market and just realized that my board isn't compatible. And I'm wondering, will it work if I connect my floppy drive to a cf card reader which has same number of pins? I know it's silly :p
Unless your CF card reader was built to be plugged into a floppy interface, no you can't.
A floppy drive interface is fairly "dumb". It requires the controller to do everything, such as individual motor stepping and interpreting the analog read off the disk.