The likelihood of D2 shorted is pretty small. D3 may be damaged because it’s a zener diode, and if the voltage presented on it is way above 5.1V it will be burned. So try to take off D3 first (just cut the leads from the front side of the PCB, you can always re-solder a new D3 back by soldering it from the front side of the PCB).
The likelihood of PCB trace problem is extremely small: all PCBs have been 100% tested. We use the same manufacturer for assembled OpenSprinkler boards and have not encountered any PCB trace problem so far.