Great to hear that you were able to get into the BIOS with the new keyboard - too bad that a new battery and restoring the BIOS settings didn't resolve the issue.
With this out of the way, my guess is that the desks locks up the moment it tries to engage word clock sync from the clock card (because that gets activated pretty much at the point once the desk is fully booted... so, having the mouse respond for a moment and then having everything freeze, sounds like it happens when the desk starts looking for clock (internal or external).
One possible cause, would be what the word clock setting is set to in the startup session. It shouldn't lock up because of this, but if the startup song has this set to "external" clock that isn't present (and something else is wrong that causes the freeze), then I could see the startup song as a potential cause of the issue.
So, with the USB/IDE adapter, I'd just open the rack unit, but keep the spinning harddrive in place, then connect the USB/IDE adapter to it via your every day computer, then find the startup song and delete it.
Then I'd connect the drive back to the D8B computer, and try booting another time.
If you're lucky, it might not freeze anymore after that... but I suspect that it's not just the settings in the startup song, but likely word clock not reaching everywhere it needs to (e.g. either the solder spots on the Apogee clock card I mentioned, or bad contacts, elsewhere.
You do make a good point about the problem likely happening in the rack unit, rather than the console, since the same thing happens with another console connected. However, the clock ALWAYS gets generated in the console (via the stock or Apogee Clock card in the "SYNC" card slot), and then sent to the various components in the console, but also back to the rack unit.
So, if the lockup also happens with the other console (did that also have an Apogee Clock card installed in it), then I'd focus on first cleaning any connections on the way from the clock card to the rack unit.
Did you try what happens if you try booting the rack unit without any console connected at all? At least in that scenario, I'd expect it to boot to the same place it went for you, so far, but then instead of locking up, it should give an error, such as "Last Status: DSP card not ready" (although I'm not sure if OS3 typically does that... OS5.1 would definitely show this message)... but I think the mouse should then still move, instead of freezing.
If this is what happens with no console connected (Error message, but mouse still can be moved, although you can't "do" anything with it), then it would once again point to the word clock not being distributed everywhere it needs to go, IMO.
If it locks up all the same, then I'd have a close look at the power supply components inside the rack unit, to see if anything seems odd, and also reseat connectors and clean them.
...at least that's the stuff I'd do first, before doing the full ribbon cable reset in the console, etc. It's probably a good idea to do that, anyway... but I usually like to take one step at a time and then check for changes in behavior, to get a better clue where the problem actually came from (...and know better if something similar happens, again).
As for what Phil mentioned about the ribbon cables... (I hope I'm not beating a dead horse) - the way the connectors are attached to ribbon cables is, that within the connectors themselves, there's these metal spikes that pierce through the ribbon cable at the right distances, to make contact with the wires inside.
...and sometimes there's oxidation, where those spikes touch the wires inside the ribbon cables. So, short of replacing all the ribbon cables with new ones, it can help to clean the spikes/wires inside the connector.
I mean, from my understanding, Mackie had issues with these ribbon cables from early on with the D8B. So, not the best contact in the first place, I guess, and then maybe not the highest quality materials in the connectors (i.e. probably went for the cheapest vendor for these cables). I think that's why the ribbon cables in the D8B need more maintenance than ribbon cables in various other equipment of similar age, usually do.
So, to summarize, I'd first delete the setup song to make sure that doesn't cause the lockup. Then I'd take a good look at the components on the Apogee Clock card (i.e. SYNC slot - if it says Apogee but isn't in the SYNC slot, then that's likely not a clock card. DIO8 I/O cards also say "Apogee" on them, for example), to make sure no components are trying to fall off of the card (i.e. re-float or re-do the solder points, if so).
Then I'd look in the rack unit's power supply, to see if anything isn't right, and clean a few of the contacts while at it... (and also clean the BFC connector contacts, while at it).
Once I checked all of this "quick and simple" stuff, that's where I'd look at doing the larger tasks, like reinstalling or cloning the Mackie OS back onto the spinning drive (or a new CF card), or doing the full ribbon cable reset.
I think if you go about this with the expectation that you might well have to do ALL of these tasks before having a fully working desk, then you shouldn't get too disappointed... of course it can happen that such a desk doesn't want to be brought back, somehow (i.e. see csp/David's thread)... but most of the time, when patiently working through all of these "typical" D8B maintenance/ressurection steps, it should eventually "come back."
Just keep your patience up, and your expectations low to avoid frustration, haha
Again, best of luck in the meantime!