OK, well part of the problem seems to be with z-index properties (these are used to make certain elements display above or below others, to let web designers essentially stack parts of the page on top of one another).
What seems to be happening is a piece of Javascript – based on what you’re telling me, it presumably ships with your theme – is applying all of these z-index values to a wide range of elements after the page loads. That makes it very difficult for us to give you for example a CSS snippet to workaround this.
Given this problem, would you be able to approach the theme vendor and ask why this happens/why it’s necessary and if they can identify and strip out the code that does this?