Hi, I am on vacation this week and I will give you some quick troubleshooting suggestions to hopefully help you figure out the issue.
First, from the pictures, I couldn’t tell if the three pins of the power switch are soldered reliably. It looks like there isn’t much solder on those pins. So try to resolder these.
Seccond, if the voltages are wrong when the controller is powered by USB, that most likely means a shorting somewhere. You should measure the resistance between VIN and GND, also VCC and GND. They should be at least on kilo-ohm level. I won’t be surprised that yours shows only a few ohms.
The exact cause for shoring could be complicated. But I suggest that you first take off MC34063, measure the resistances again, and then if there is still shorting, desolder (or simply clip off) MCP1702-33 linear regulator. Let me know your discovery after following these steps.