Thanks for the recommend on the PCB layout app.
Big NO on losing the USB. As stated, this is for my personal use, so I have no constraints on size. Also, I'm keeping the scalability. So sticking with the UNO.
I baselined the whole thing on a Mega, so it's already coming down in size. As a newbie to this, I want to keep this particular layout as easy to upgrade, as possible. Arduino and clones are so cheap, I really see no reason to shrink this to highest degree. It just has to be tidied up.