Custom 32u4 pcb program's fine, does not start.

Are you sure you're checking the right pin for the blink? It's common for people getting started with working with bare microcontroller chips and Arduino to not understand the way Arduino pin numbers are mapped. Arduino pin numbers are arbitrarily assigned and don't necessarily have any relation to physical pin number or port bit number. For example, if your Blink sketch is blinking pin 13, that is PC7 on the chip.