The part of the capital city I care about is unclickable, offscreen, or covered by the store

Some parts of the Capital City's user interface permit mouse interaction and some do not (please refer to the screenshot above.) If you click and drag within the red area outlined in the screenshot, your mouse pointer will turn into a grabby hand and you will be able to scroll around your the map. Scroll the map so that the part you're interested in moves into the red outlined area. Then you will be able to interact with it normally (place buildings, harvest earnings, etc.).