Edit: Oh wait, also make sure you have "Ghosts In The Machine" selected when you go to the signal tower!

Yeah, the "show the Atlas a wonder" quest is repeatable and endless, same for Base Computer and Settlers, so you've completed those questlines (at least, Atlas and I'm pretty sure Settlers - Base Computer might offer more as you progress the Artemis quest line).

As to Ghosts in the Machine, that signal tower you get sent to should have someone to talk to at it. I don't think it's possible to have missed something with that quest in your log, because talking at the signal tower is the very first part of it.

If you select the Ghosts In The Machine mission, there's a way to restart it "with local objectives" or something to that effect. I'll see if I can find how to do it when I'm back at my desk - the internet is being unhelpful right now.