I think source menu goes to the menus where you select systems/tiers and source flow is where you select games. So our problem is probably source menu related.
For the source menu setup being I can't think of a solution, but for the other buttons on screen you can change them to blank .pngs, (I've done this with my theme, I'm gonna put some images)
You can edit the text on the Wiimpathy's system.xml with a text editor, or just use it as a base to create your own.
Sometimes we have to work a lot to configure it the way we want, but Wiiflow is really awesome. I really love it <3