Another big shoutout to Anthony for helping me out big time!
Anthony's "They don't teach you this in school" technique for keeping the drill in the right place using a cloth hanger.
This is the final product of the external box and my take at the BeanAnimal's overflow.
Hacked together fittings and strainers I had around and I think it will work, I hope... Cutting tiny parts in a straight line is hard...

We were working with a bit that was starting to get dull and the first hole took much longer than when we drilled the tank so I decided to go with my original design so that not all 3 holes would be on the same panel.
Tank prepared to have the external box siliconed on.
Now I just need to clean everything and plumb the tank once more and I'll be done with the build! I hope... haha