Unfortunately, you cannot do everything with CSS frameworks. For that, they would need basically as many options as pure CSS styles have, which makes them pointless. You, are going to have to include some styles of your own. Personally, I use BootStrap a lot, but only for positioning; if ever there is a colour/style i want to change, I use CSS.
As for your “missing” border. You need to use CSS for this, and have a focus selector change the z-index of an element, to ensure the border is not behind the adjacent elements.
Hope this helps