How to localize cause of short circuit in proto board design?
You mentioned using a small housing, ensure that the compact space isn't causing any components to bend and touch each other when the unit is assembled and closed. Look for any exposed leads that may need a bit of heat-shrink tubing around them to keep them isolated from other nearby components.

I'd recommend using a multi-meter in the continuity test mode and validate all the wiring to ensure the circuit matches your schematic exactly. Also check for continuity between things that shouldn't be connected, like a power rail and ground.