Sorry for necromancing old post but revival such good SBC is a priority.
D5 you mentioned indicate that there was too high voltage in IPSOUT circuit which is internal 5V generated by U4 AXP209. You need 5V 2A power supply with current reading, if nothing is getting hot and current is under 1A, first step is to check if U4 is generating 5V on IPSOUT pins. If not then with power off check if there is short circuit IPSOUT to GND. If yes, connect power supply to IPSOUT and GND, 5V 1A limit, something should start getting hot - replace it and restart testing.
It can be fatal in the end as overvoltage passed through U4 (it can be dead too) and could kill literally everything.