Please find the schematic of ArduinoMEGA and tell the connection of IOREF, ... connector pins?
IOREF only connects to 5V, it's to tell 'smart' shields the level the IO is using - 3.3V, or 5V.
On a Due, it connects to 3.3V, on a Uno/Mega it's 5V.
If you want access to all pins, I have a couple MiniMega boards available.
This one now
http://www.crossroadsfencing.com/BobuinoRev17/
Top
Bottom
and this one I just ordered boards:
https://forum.arduino.cc/index.php?action=dlattach;topic=455570.0;attach=200083
3.3V regulator, '2560 Rs, Cs, Xtal are on the bottom.
Add a right angle header for an FTDI Basic.