[Darryl Ramm]

Everything is pointing at a dead port 2, as you know.

When troubleshooting Digilink it's always a good idea to simplify as much as possible and I'm pretty sure there is no need to populate stuff on port 1 first. So get one box working on port 1 no other boxes chained to it.

Then take the digilink cable on port 1 and swap it to port 2. Don't undo the cable into the interface box or mess with anything. Don't add any other boxes or cables and no need to mess with loop sync cables (disconnect them). Try some gentle wiggling of that mini-digilink port 2. Always worth looking carefully at a card where these ports don't work to see if you can see damage (but here that would mean opening up the Thunderbolt box don't do that if you have a return option on it).

Power on sequence does not matter in normal setups, this TDM (or strictly TDM2)/Digilink bus protocol is as dumb as a box of rocks, and again all the debugging you need to do can be done with one cable and one interface box, so do it that way.

But because it's a Thunderbolt HD Native box there might be additional suspicion about the power supply to that box.... what Thunderbolt 3 to 2 adapter are you using? Especially if Port 2 works by itself you might want to try powering the HD Native Thunderbolt box with a seperate power supply.