I have a suggestion.
I didnt get a chance to read all of this thread, so it may have been said already.
I think you should include a cover for the side of the case where everything hooks up. That would create a suuupperr clean install. I real quickly used paint to show you what i mean. It would consist of the side, top and bottom edges, and a top or it could be covered by the lid as well....

I see this design a lot with amplifiers.
then the wires can be bunched and evacuated out the bottom. I also think the power wires would go through the left side and out the bottom of the added portion.