Cutting a slot in a PCB using a hand file for a USB connector - are the planes exposed and shorting with the connector?
Several potential issues exist that I can see.

Firstly, your "decoupling caps" should be as close to the pins they are inteded to decouple (usually the IC power pins). This can cause all sorts of weird behaviour in digital circuits.

Your D+/D- diff pair is not routed with constant spacing, which could cause signal integrity problems due to impedance mismatch. Although if its a low speed device that is much more forgiving.

A third thing, in the photo of your connector, there appears to be a short between one of the data lines and the ID pin. If the cable shorts ID to ground that would cause the data line to get shorted to ground. Check your soldering, reheat the joints with a bit of flux and examine under a magnifying glass or microscope. You can also use a DMM to probe for continuity to check for shorts.