The controller is designed as double-sided PCB with 95x55 mm dimensions. In this PCB version has so low number of vias, component and traces density that makes PCB manufacturing possible even in home environment. There was no goal to minimise PCB dimensions but to make as much easier as possible to replicate it.
All components are mounted on the top side. It is recommended to solder 40-pin DIP socket instead of AVR chip itself to leave an opportunity to replace the chip whenever it is necessary. Y1, Y2 are better to be placed horizontally insulated by PVC sections. Length of LED1, LED2 pins should be adjusted to fit inside controller's box and be long enough to reach box's front panel. To prevent PCB bottom foil detachment LED1 and LED1 pins should have PCV sections put on.
PCB tracing and component layout is given below: