Making electronic prototypes [recommendation]

When your are designing a prototype, move slow. If you move quickly sometimes you will find some problems. For example if you are going to put your proto PCB on an enclosure, it's a good idea to choose a box somewhere close to you, buy one unit and then try to fit the pcb on it.

Always work with real models. Order some units of your proto pcbs to phisically test and mount in the real box. Sometimes you will use the first box, sometimes not. When you see it mounted perhaps you will get a new idea about it. Let your mind explore, touch and imagine playing with real models.