Hallo Steve,

I fear that you highly underestimate how skilled a floppy controller does it's job.
I have a circuit from 1983 here, built arround FD1797. There is a complex data separator circuit in it consisting of 9 chips! And there's need for very carefully adjustment!
Data separator is necessary to deal with high data transfer rate. It's absolutely necessary for achieving synchronizing. Don't forget that data transfer rate is 250kbit/sec! Having synchronising without PLL data separator seems to be possible, from a theoretical point of view. But then you have to handle this high data transfer rate...

You write, that you need not having this high data transfer rate, not even the high capacity of 1.44MB, and so you think it must be possible to work without floppy controller and without PLL data separator, just with a simple microcontroller.
But unfortunately this will not work! Analog circuitry in floppy drive is very complex and in order to compensate for DC levels at some points in circuit certain filters are implemented with certain time constants. And theses time constants are well matched to standard data transfer rate. So, if you would slow down data transfer rate, the floppy drive analog section would not be able to produce correct flux change signal for writing on floppy or to recover data from flux change signal when reading it.
So, you will need to work with standard data transfer rate, and because of this you will need to work with highly skilled PLL data separator.

Bye,
Kai