I had a defective 828. It would click on occasion. Got it replaced, and it was fine after that. Click = digital glitch. They show up as tall full sample lines on a waveform. Can't miss them with your eyes OR your ears. So, give it a listen. If it sounds fine, it is as fine as it ever will be.
I'd used the spdif ins and outs for years back in the system 9 (mac) days, mostly going in and out of a dat player digitally. This was the orginal 828, btw. Once i got the initial problem worked out, I never had any problems related to the 828's digital i/o.
I've heard the firewire to pci argument before too. If it works, it works. You won't get 48 tracks out of a single firewire400 interface though.