Darren,
The AirPort Exteme (AE) is one of the older 'space ship" styles. Perhaps because it's older, this is the one I have the most challenges with. My setup is stable and robust but a few times this year (about once a quarter), the AE has gone off the grid. Power cycling it resolves the issue.

Since I wrote this article I've found it easier to set things up from the WDS main which for me is the TC. I would suggest reseting the AX to factory default ( you can find documentation here at Apple) and then enter the WDS Remote information into the WDS main. Make sure to write down the IDs of the AX before configuring.

I'll try to make time to update this article with update information based on my findings.