Schematic
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PCB rev.A
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Add diode 1N4148 after R18 into P2, minus facing R18.

Fix switches SW1-4, connections wrong. Check libraries
connection between schematic and pcb.

Fix FT232 power, skip crystal X1 and C3. VCC must come
straigh from the USB connector while VCCIO connects
straight to  3.3V, skip JP1 and JP2.

LED's D2 and D3 are in the wrong pins, move them to pin 13(PB1)
and pin 14(PB2), no specific order, whatever is best for routing.