Where can I find correct documentation of old floppy drive formats?
I would check usenet comp.arch.fpga as there have been several projects aimed at making fpga boards that run a favorite old CPM, Tandy or Apple II machine. 
Another possibility is to use a piece of hardware to emulate a floppy assuming you can recreate the files stored on your disks. 
Look at http://www.thesvd.com/
If your piece of equipment uses both a disk I/O and file format like one of the supported pieces of hardware, this would save you a lot of trouble.
Jim Sather's book Understanding the Apple II+ gives a detailed description of both the circuitry used in the Apple's disk II controller (it was a state machine made of a 555 timer a small bipolar prom and a few TTL parts. There was a second prom for a boot loader)
There is also a great deal of explanation of the 6502 routines used for disk read write I/O.
Likely that information would only be minimally helpful as a starting point if you were forced to make a solution from scratch.
The early Apple Lisa and Macintosh machines used Sony 3.5 drives, so projects emulating those boards will likely work as a drive controller with the drive, even if the disk formatting is different.