I'm a long-time MIDI musician who is self-taught in all things recording. I'm a professional software engineer by day, so I know a thing or two about a thing or two, but I'm not a MacOS expert by any measure. Indeed, as a computing professional, I find my ignorance of my Mac to be especially frustrating considering how much I know about certain other systems, but how many different systems can I be an expert in at once and still have a social life and time for music-making? Right. Ok. On with my question!
So recently I decided to go nearly-all-digital with my live recordings. I have this lovely Rode NT2A mic connected via BLUE quad cable to a Focusrite TrakMaster Pro preamp with an internal A/D board. That A/D board spits out S/PDIF over a short high-grade coax RCA cord to my MOTU 828. Yep, it's an original unit from when the 828s first came out. Version 1.01 or something like that. The 828's clock is slaved to the TrakMaster Pro's S/PDIF stream, as configured by Digital Performer 5.12 under "configure hardware driver". The TrackMaster Pro and the 828 are both set to 24-bits, 48kHz. The 828 speaks via FireWire to my twin-engine 2.3 GHz PowerMac G5 (6GB RAM, dual 250GB SATA drives with plenty of free space, the OS on one, the recordings on the other) which was running the next-to-latest drivers from MOTU at the time. I do have two FireWire devices - the 828 and a Memorex external DVD-R+W drive - sharing an 6-port IOGear brand externally-powered FireWire hub.
My problem is that this system routinely gives me drop-outs in recorded audio, occasional click and pop noise which appears to be corrupt data packets when inspected close-up. The noise is sometimes superimposed on what looks like a good signal and sometimes it's just crap. The bursts are short - tens of milliseconds or shorter in most cases - but they certainly disrupt the audio, making my post-production editing a much bigger job than it needs to be. The problems do NOT appear to be single-sample in duration, but a bit longer. When I first set this all up, I didn't have the 828's clock synch'd to the TrakMaster Pro, which gave me tiny clicks all over the place. I fixed that some time ago and proved it by recording and then inspecting a few minutes of pure sine wave through the air and back into the system.
I'm at a loss for how to investigate and diagnose this problem. I do have an oscilloscope (and I know how to use it). I don't have many other tools other than the usual recording gear in my rack. I believe my power is relatively clean, though I am not using a "power conditioner" of any kind beyond the filter provided by my UPS (an APC BackUPS XS 1000). The UPS battery is for the main computer. I use the pass-through outlets, which are filtered/surge protected/etc, for the rest of my gear.
Looking for advice - specific instructions aimed at a smart, but ignorant guy

I do remember having stuck MIDI notes some time ago which turned out to be the fault of a cheap USB hub... admitedly, I have not exhaustively investigated this problem with and without this FW hub. I should probably do that, in addition to whatever other advice you might be able to offer

Thanks much!
Daniel