From the things that I see, the problem lies in the way you use custom modules. Everytime you insert even a image, it is wrapped with paragraph. And paragraphs as a typography element has bottom spacing so they look fine when you have more then one of them. Now this spacing overlaps spacing of entire column, so you cant get the spacing exactly you want.
The solution would be to disable tinyMCE editor for a while, and edit modules that are last in each column (content, sidebar), then manually remove wrapping paragraph from the module.