Lesi, The map journal app does not contain a file the specifically controls the popup experience. Instead it relies on the default popup experience that is built into the JavaScript API for the webmap.
I would actually encourage you not immediately open a new tab when a user clicks on a feature in the map. That is not the typical behavior of a map application (arcgis map or other maps applications online) and may cause the user the get disoriented. It also drives the user away from your story and they are not likely to return. Instead, I would recommend creating very simple popups the include the title of the feature, maybe a simple description and a small photo that is a link to the website. This allows the user to explore multiple points then, when they are ready, they can open the new tab for more information. Here's a story our team created as an example: http://storymaps.esri.com/stories/2014/brazil-beyond-the-stadiums/. The soccer ball icons contain links to information about the soccer stadiums. These popups can easily be created through the ArcGIS Online map editor.
