Studying the picture of the terminator that was installed on the Diablo drive for the Alto, I see that it has almost no resistor terminator pairs. Five signal lines are terminated, but only two are actually used with the Alto - ReadData and ReadClock.
These pairs pull the line up to +5V and down to ground but provide a characteristic impedance to terminate the transmission line that each cable wire acts as. None of the lines out from the Alto are terminated and the only lines going into the Alto from the drive that are terminated are the two I mentioned above.
My board was built based on the Diablo drive documents and recommendations, thus all the lines have termination on my end. I will now remove all those resistors, except for the two pairs used with an Alto.
I should mention that the Alto has two pull up resistors on the disk controller card, but these are for the FileReady and SectorMark which assures that a unpowered or unattached drive will not be seen as ready or drive any dispatches of the DiskSectorTask. These are not providing impedance matching.
Using my hot air rework gun, all the resistors except for ReadData and ReadClock were yanked. As far as I can trace, all signals go correctly to the fgpa connector on one side and the IDC connector that hooks to the Alto on the other. No shorts or miswiring, as far as I could tell
As a final test, I tried to hook the board up to some power supplies and checked the behavior of all the signal lines. That is, I will provide +5V and 0 values to the input lines and watch the FPGA side for appropriate output voltages (3.3V and 0). I then apply +3.3V and 0 values to the FPGA side output lines and monitor the voltages (0 and 5V) on the Alto side.
For some reason, I couldn't find the connector to provide the +5, +3.3 and ground power to the board. It is a four pin Molex just like the power connections to older hard disks (e.g. IDE disks). I have thrown out excess items and packed up much of the rest to allow me to remodel my back room office and work in the garage. I will need to go out and buy a connector tomorrow then continue the testing.