Always open to ramblings
I have experiencing in manufacturing - so creating something custom for prototyping won't be too difficult.
Flip the switch orientation so that the switches are facing the other way. The switches are designed to be used the other way, and if you leave them like you have them (north facing), some types of keycaps will actually hit the switch and that is a very bad thing. Also if you orientate them correctly then if you decide to add in-switch led support down the road, the leds will be facing the correct way (south).
The usb port needs to be on the top of the pcb (the top is the side the switches are on) between the f12 and print screen key. This is called the a.87 standard. And this will free up a lot of compatibility for you.
From there you could figure out your stabilizer hole situation. As you have it now, you can only use plate mounted key stabilizers on the large mod keys. No one uses plate mount unless you are an OEM. Diy people use PCB mounted stabilizers.
From there, bring in the foot print in as far as possible basically. Theres not a ton of room inside these custom cases.
Pick up a TKL pcb from txkeyboards.com and study the **** out of it.