Of all your measured voltages, 2.16V on the rightmost pin of the 5V connector is the most bewildering. ?That should be the PWR_HOLD signal and either 0V or 3.3V as it's driven by the CPU.
Hans has stated that the bootloader does not enable the SMPS and only runs off the linear regulator (
/g/QRPLabs/message/106572).??Have you looked over the 3v3 board to make sure the linear regulator is running? ?LIN_REG_EN (the middle pin on the top) should be higher than 0V when switched on and you should have ~3.3V at D103.
It certainly seems like there's a short or bad connection somewhere that might be pulling the 3.3V rail down and preventing the processor from booting.
Jonathan KN6LFB