Really curious what they find out about the disk, nothing at all coming over the interface sounds like a big (and usually simple) issue, like card in the wrong slot or cable plugged in backwards or to the wrong connector.
To clarify the disk issue, we're seeing sector pulses coming from the disk drive, so the drive and cabling is working. The Alto isn't sending any read requests to the drive, so it seems most likely that the microcode isn't seeing any disk request block in memory.
A lot of things need to work correctly to get the request block into RAM. So it could be a problem with a chip on the ALU board, a bad memory chip, something wrong on the disk interface card, a corrupted bit somewhere, or anything. With the logic analyzer, we should be able to see at what point in the microcode things go wrong. The nice thing about the Alto is because it's all TTL chips, it's straightforward to see what's happening.