While waiting to find/buy a new USB cable with a better fit to the fpga board, I can't run the disk drive when the fpga is randomly resetting or emitting incorrect signals. I will switch over to debugging of my emulator role in the interim.
Unfortunately, the situation with the connection and the fpga board is bad enough that I couldn't get the board to respond even in emulator mode. I se up a few diagnostic signals and synthesized so that I could look again when I returned from my day with the 1401 restoration team at CHM.
I found another cable and had the same very erratic behavior with the board. Since I have another fpga board, I used that instead but it is the 1200K gate version, not the 500K gate variant. Something is wrong with the USB link on the 500K board.
I had to resynthesize for the 1200K configuration before I could test the new board. This also required some config changes to the UCF file because the 1200K version of the board hooks four of the LEDs to different FPGA signals than with the 500K board.
I began testing the emulator function, slowly working through the logic to get it working. Glad to be moving forward again. I also have a reliable board now which will let me hook up the new driver board and test it out.