Damn I go get something approaching sleep, and you cats write a novelette!
Word Clock is simply to reduce jitter, (jitter is real I tell you!), but great find on the jumper. I had completely forgotten about that one! There's just too much!!!
SPDIF ports are notorious for blowing out. Always (I know I've done it myself) power down at least one if not both sides when connecting SPDIF ports. A decent grade audio cable should be fine for SPDIF. Maybe not the cheapy consumer radio stuff, but I think I've even used those in the past.
The code from SPDIF will be the same, it's also the same with AES (for all intents and purposes).
Do you have another box with which you can test? I always like to create a test positive when things are being weird. But yeah you gotta get all the ducks lined up. You have to have the correct sample rate, the right ins to outs, the software setup in multiple places, etc.
Did you tell us what software you are using yet? Like the app, version number, associated apps (like DAE). I looked, but didn't catch it. Those things do matter.