Let's go about this one problem at a time, or it will get too confusing. Let's get the D8B and your Pro Tools system synced up first. Have you tried what I suggested, yet?
Generally, though, if all the digitally connected equipment you are using is NOT synced to the same clock source then you can't really use different types of digital inputs and outputs between different devices at the same time (e.g. S/PDIF and ADAT). At least you'd get problems such as pops and clicks if you'd try. Older Pro Tools systems might also have a limitation when it comes to that (or share the same optical port for S/PDIF and ADAT... but I think the S/PDIF on the 882/888 units was RCA), but I don't remember. You'd have to read up on that online.
So, again, let's get the D8B and Pro Tools system synced up first, then we'll look at the other questions you had.
If the D8B is clock master, then you will NOT take advantage of the good old Digidesign "Superclock", though. In that case, the Pro Tools system will sync to the D8B's "regular" Word Clock, that runs at either 44.1 kHz or 48 kHz. So, that advantage is gone (and overrated anyway, IMO).
Someone else here may be able to answer this, but IF you had an Apogee Word Clock card in your D8B, it might not even be able to sync up correctly, if you'd have the "Superclock" active and sent to the D8B via a Word Clock cable - not sure.
As far as I know, external Master Clock devices, such as Apogee's Big Ben DO support the Superclock, but have the option to configure individual Word Clock outputs to send a regular clock signal at 44.1 or 48 kHz instead, that devices without Superclock can understand. So, the Apogee Big Ben should be able to run your Pro Tools system on Superclock, while also outputting a lower version of the signal to sync up something like the D8B. Not sure if you can do that directly between a TDM/Mix interface (or the Universal Slave Driver) and the D8B.
What Converter Box are you actually using with your TDM cards?
About your opinion that an old Pro Tools TDM system still sounds better than more modern systems... if you like it, great! Let your ears be the judge!
I happened to have worked at Avid for a few years, though, and they gave me a HD2 system for free (that's why I had the 96 I/O converter box). After trying to use it for a few weeks, I started HATING "digital" because the sound was so abrasive, stopped working on music, and only listened to pure analog signal chains for a while (e.g. turntables to phono-pre, to active speakers). After trying a budget M-Audio interface I had lying around, I noticed that this wasn't even nearly as abrasive sounding. So, I didn't actually hate "digital". I just hated the converters in the Avid 96 I/O (I was told the 192 I/O converters and newer HD I/O converters are much better sounding, but haven't worked with them myself, so I wouldn't know).
Many years before that, I had a Digidesign Session 8 System that used an 882/20 (same as what Pro Tools TDM/Mix uses out of the box), plus an ADAT Interface/Bridge and two ADATs, for 24 channels of I/O. Even the ADAT converters sounded better (if using the ELCO multi-connector to get balanced I/O) than those in the 882/20, so I recorded through those if I didn't need all the channels at once, and transferred the signal digitally into the computer afterwards (this was possible via the Digidesign ADAT Interface - albeit in real-time. You had to play back the whole recording (8 Tracks at a time) at regular speed to transfer to the computer... but the better sound was worth it).
As mentioned, the 882 generated clearly audible quantization noise... a low volume "digital sizzle" that was always present and could even be heard on my relatively noisy analog D&R Series 2000 console I used back then (...and even more so on the Alesis X2 console I replaced the D&R with a bit later... but the Alesis board had it's own set of (grounding) problems).
Personally, I do NOT agree with what you said about the sound of an old Pro Tools TDM system, though, sorry. Even budget converters in simple (but modern) $100 audio interfaces usually sound better than the 882 in my opinion, and definitely don't have audible quantization noise (same goes for the 888 since it uses the same converters as the 882 from what I read today). As mentioned, I thought my 882/20 was broken and returned it twice... but the replacement sounded the same (I even got the power supply replaced, thinking it might have been that - but no). So, the sizzling was part of the 882/20 sound
If you are using one of those Apogee or Prism converter boxes that were available for Pro Tools TDM/Mix systems back then, then I wouldn't know how they sound. Never got a chance to try them. But they're most certainly better than a stock 882 or 888. Not sure how those hold up against modern converters, though.
But again... if you like it, by all means, keep using it.
I also tried to use Cubase XT 3.0 with the DAE (Digidesign Audio Engine) back then with the Digidesign Session 8 system and always had problems with that. Wherever I made edits, it created a click (it didn't find the zero crossing, even if I had turned the "find zero crossing" feature on in Cubase), and there was no solution. That's why I switched to Logic Audio 2.4 in the late 90's, because Cubase on Digidesign Hardware just didn't work right. Logic Audio 2.4 supported DAE, too, but had it's own problems, so I eventually moved away from Digidesign hardware altogether, since I was just not a fan of Session 8 (or Pro Tools for that matter). The MIDI options in Pro Tools in those old versions were a joke, compared to what other DAWs like Cubase or Logic were doing.
A bit later, Digidesign stopped supporting the use of other DAWs with the DAE altogether, until about 2008 or so, where Pro Tools was opened up to M-Audio devices first, and later to any brand of audio interface.
What version of Cubase are you using with the TDM/Mix system? I thought DAE support kinda ended with Cubase 3.0, no? But I didn't pay attention to that much anymore, when I moved away from Cubase back then.
...and in terms of latency, I use a PreSonus Quantum audio interface that gives me under 1 ms latency when using Studio One. If you look at the specs for the old TDM chips, the latency is higher in those (...even though the claim is that they're 0 latency... the hardware chip actually DOES introduce a small amount of latency, too).
So, overall... if you like your system and you're having fun with it and get good results, great! But it really isn't a match for modern hardware anymore, in my opinion, sorry!
Having said that - I wouldn't use the D8B, if I wouldn't have a thing for old hardware. So, I think I do get the excitement of resurrecting an old recording system and using it again
I keep several generations of computers around to do exactly that (old G4 Laptop with OS9, old G5 Tower, Pentium with ISA slots (like in the D8B computer), etc.
Anyway... let me know if syncing your Pro Tools TDM rig to the D8B's S/PDIF output worked. Then we'll take it from there.
Again, best of luck!