The serial output of the Apple's floppy disk drive produces a continuous bitstream where one bit is output every four microseconds. Generating this bitstream has been more difficult than I had expected. The difficulty comes from doing the hard drive reading, data conversion and output of the bitstream all at the same time using the existing resources. The output of the bitstream requires a fair chunk of the CPU time just by itself. I was unable to utilise the Atmega's USART as the start/stop bits can't be disabled so bit banging was the only other option available. Adding some extra processing power will be required.
Another shortfall is the amount of available memory. Presently there is only room for a few sectors to be buffered. By emulating a spinning disk, a given track's data is output again and again. This causes the hard drive to read the same sectors over and over again. Being able to buffer an entire track would save wear and tear on the hard drive. Extra memory will also allow me to write a better implementation of FAT.