1) Does S/PDIF get routed through the digi cable to the Apogee? On the 001 it is directly on the Digi card.
Yes, All digital info travels through the digi cable to the converter.
2) Where the hell do I route to get audio to the powered monitors? On the 001 there is control room out on the interface. Would it be possible to get S/PDIF out of one Apogee box to the PSX 100 and listen from there?
On the MIX+ there is no separate CR/Monitor output, think of it more like a multitrack than a workstation. There are several montor solutions out there, from the inexpensive (i.e. Mackie) to the high end (Martinsound, Crane Song, API), depending on what your budget can handle. Of course there's also the full console option...
4) Finally, I'm thinking I will need a Big Ben to clock the whole shabang. Word on the street is it will give new life to the 8000 SE - do you believe or would you dump it for another Rosetta
Big Ben would definitely bring a new clarity and definition to your 8000 SE. I would take the clarity over additional I/O, especially if you are doing a lot of "in the box" mixing.