I am powering my HK Mega board from an adjustable power supply connected to J10 - D46, edge of board is GND, next pin away from board edge is positive supply input in my case..
With 5V input, 5V=3.91, 3.3V=2.83
With 6V input, 5V=4.88, 3.3V=3.33
With USB disconnected VBUS LED is OFF, 5V LED ON RED, LED2 BLINK, LED3 BLUE. LED4 OFF.
Quit worrying the low voltages are normal, Low Drop Out [LDO] voltage regulators are used which explain the drop, the slightly lower voltage does not affect any of the sensors or GPS or ATmega2560 as they are all rated below those voltages.
If you want exactly 5V and exactly 3.3 volts then power it with 5V input at the 5V pin on J2
Uploading twice to either 3DRadio station does not cause any permanent problems.
The 3DRadio, try this - power the HK Mega board up with the 3DR radio NOT plugged in, once LED on HK Mega blinking - then plug 3DRadio in, then try to connect, if that works the issue is handshaking CTS and RTS on the 3DRadio.
are you sure you have the correct COM Port and Baud rate ?
Try these setting for 3DRadio