Bill -- That's a pretty good description of what's going on.
What I don't know is the sequence of the tubes - e.g. anode 1, cathode group 1 is the high order hours digit (or the low order seconds digit), etc. Each combination will correspond to a time data element - you may have to play with that and you can always adjust it in the Arduino code.
There isn't a specific answer to that, because the ArduiNix doesn't have a predefined sequence. The sequence is created in the code.
For my clock, I chose:
A1 C0 - Hours high (tube 0)
A2 C0 - Hours low (1)
A3 C0 - Minutes high (2)
A1 C1 - Minutes low (3)
A2 C1 - Seconds high (4)
A3 C1 - Second low (5)
...which lights tubes 0+2, then 1+4, then 2+5, repeat.
But you can choose any sequence you can code.
I also built my own board and tube harness.
https://plus.google.com/u/0/photos/113825690086131396297/albums/5728271875401245617/5728271876241407938?pid=5728271876241407938&oid=113825690086131396297https://plus.google.com/u/0/photos/113825690086131396297/albums/5728271875401245617/5865387316409291922?pid=5865387316409291922&oid=113825690086131396297The harness photo didn't yet have the anode wires attached. I definitely recommend ribbon cable to keep the cables managed, but as you can see in the album I trashed the salvaged IDE (computer) cable I started with.