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Odds are just one cap is shorted somewhere. If you don't have access to a thermal camera (I know I don't) you can put a couple of drops of rubbing alcohol on the board here and there and then power it up and look for where it evaporates from first.
All U1 does is take the 5v from the USB and regulate it down to 3v for U2 and U3 to use. The top board is where the 3.3v is made, but the bottom board uses it and whatever is causing the 3.3v reg to heat up will also be getting warmer than it should. You can take the top board all by itself and plug it up over USB and test to see if all of the voltages from it are correct. Measure the voltage across..C8 = 3vC15 = 3.5vC22 = 3.3v