The display fits very snugly so I will let it be for now. I will likely drill out the corner holes and install screws to keep things in place.
The rotary encoder will be mounted to the right of the display. In reality, with a single line of code I can flip the rotation of the display by 180 degrees so it is easily adaptable to left or right handed operation.
I have been considering how to implement a single control interface using the rotary encoder and its built in push button. I think that I will use a single press of the encoder knob to cycle between the three clocks. The active clock is the one displayed in yellow.
Turning the rotary encoder will change the currently selected digit of the active frequency. To change the tuning rate, I am considering rotating the encoder while holding the knob depressed to select which digit is changed by the encoder.
Otherwise, there will be a power switch and the three clock SMA output connectors. I am unsure if I will mount them on the face along side of the display or if I will mount them on the side of the case. I plan to use a small LiPo battery to power the entire device.
Overall, I am pleased with 3D printing as a medium for prototyping things like this case. The aesthetics are not the greatest, but the strength of the case and the amount of accuracy of the print to the object design is quite good. It will be interesting to see if my son's calibration efforts on the printer will have any effect on the aesthetics.