The floppy is working 100%. I thought the reading and writing from the drive would be the hardest part. I also thought that moving the head would be the easiest part. I cannot believe how wrong I was. It ended up being much easier to read and write. The documentation on moving the head states that different phases should be turned on then off one at a time. It appears that ProDOS as well as other programs turn on the next phase before turning off the previous phase. After I figured out that the documentation was wrong, it did not take too long to get the head stepping to working.
Now that I have the boot issue fixed, I am working on the floppy. I have it mostly working. I am able to use FILER to format the two drives. I am also able to store data on the drives. I can run programs from them. I can even use Copy II Plus bit copy and copy one disk to the other. But a few things still are not right. The first issue is booting from the drive. I can do a PR#6 and it will go to track 0, then it moves the head to track 1. I assume it read the boot blocks and is looking for PRODOS. I am having an issue with Copy II Plus also.