So after having researched NJ Stronghold I was searching for the new capital of NJ on the Geoscape but did not find it
Should it be a new haven, a district of a haven, just a marker next to a haven (like the marker for mist resellers) or not be present on the Geoscape at all?
I hope it is there somewhere or supposed to be there as the Geoscape inter-tie with events is one of the highlights of the game
What research exactly?
Sounds like you might’ve just misread something but anything is possible…
The research is called: “Command Fortress”
The description says “the Fortress will become the capital of New Jericho…”
Accordingly I was hoping to see it on the Geoscape and having to defend it against attacks to keep the recruitment bonus it provides
OK cool. I’ve not seen that research yet then.
On the left side you should see “Command Fortress is being built” (something like that). If you click it, it should take you to the haven where it is being built.
I’m not sure if they start building it right away, but it is very shortly after the research is done.
Once it is built you have a new mission that shows up (doing it may lock you into the New Jericho ending so you may want to save before that to experience the other endings without having to restart a campaign).
Thanks!: I just saw it on the let hand side after you wrote this and checked for it: it leads to a haven where the district is being build 
It is awesome that these things have a presence on the Geoscape