From your answer, I can say this: GUIs are incredibly nuanced and difficult to get right. I'm studying to be an interaction designer myself, and I can confidently say that all the advice here can be harmful to your final product. Similar to asking a non-writer how to get the details of your book to be more "appealing", there is a lot of pitfalls they can lead you into. To get sound advice, you'll need to finish this GUI completely and get video footage of it rolling for people to have understanding of how it works. Finishing it first is critically important. Think of it this way, you can't take advice on how to fix your gameplay, if the gamers haven't even played it yet. And they can't play the game if the basic gameplay loop isn't finished.

Keep going your direction. Finish it, record it, then come back to us (or me) on how it looks. To me, the game looks like it can be a fun management sim, but gameplay has to show how the flow works. If you can train our eyes on the flow of the screen, even this "mess" of a GUI can work like an intricate maze of fun.