There is probably a shorting or some damage on the 3.3V line. Here are my suggestions:
– Measure the VCC to GND resistance. Should be at least a few kilo-ohms. If not, there is probably shorting somewhere.
– Start by removing ATmega328 from its socket. Use a flat screwdriver to carefully pry the IC up from the two edges, and be careful to avoid bending the IC pins.
– Measure the VCC to GND resistance again. If it’s at least a few kilo-ohms now, your ATmega328 is damaged. May be due to lighting, or if you’ve accidentally plugged the 24VAC power into the rain sensor port, that will fry the mcu.
– If the problem is not with ATmega328, proceed to remove other ICs, one after another, and measure VCC to GND resistance at every step, until you find which one is causing the problem.
– If all fail, the most likely cause is the MCP1700-33 linear regulator (3-pin, shaped like transistor). Try to clip it off the board, and replace it.
Let me know if these steps help.