So, as I understand your post, you would like to run the TTL signals coming from the IC chip on the digital out board through the docking connectors on the back of the Empeg and sled. Novel approach! It even sounds like it would work. The current design has these three signals feeding into the optical module- digital ground, +5 volts, and signal. So,it would require that you give up three signal paths on the docking connector. Since the mic in line is unused, you would only need to snag one more line from somewhere else.

The other approach, docking ala ethernet, should also work. If you get the alignment right on your sled, there shouldn't be any problem. Dust is unlikely to be a problem. The current modules have a shutter, that should wipe off dust as the connector is inserted. I think that you would need to remove the locking tabs on your cable so that the Empeg could be easily removed from the sled following insertion. See my other thoughts here.

Stu