Still did not get a successful mag calibration although it was a lot better. The reason behind that is because my bec overheated so I had to replace it. Another issue popped up today as I was trying to finalize the wing: the revo suddently stopped recognizing the gps. I don't understand what the issue is but the GCS now says 'no gps'.
Probably lose connection. GPS has 4 wires, TX, RX, GND and VCC signals, TX must go to RX and RX must go to TX. You can hookup usb-serial adapter (and putty to connect to serial port COM1 with baudrate 9600) to GPS lines and see it working if you want.
Magnetometer has additional SCL and SDA lines, it does not need GND and VCC since those are already used to power GPS and magnetometer takes power from there.
You should use one of scopes to test if rotations (multiple of 90 deg) are set correctly for external magnetometer. Set one of scopes to show x,y,z for both Internal and AuxMag. When you rotate aircraft both magnetometers should show the same pattern if rotation is set correctly. Then you do calibration of both by setting to use Both magnetometers and before flying you set to use only AuxMag. The reason to set to use both when calibrating is to calibrate both, so you can see bars zeroing later on, but for flight you set use AuxOnly.
Be careful not to rip off usb connector when calibrating Mag, best is to use Oplink and doing it outdoors is a must. You can skip first 5 steps, and do all possible rotations on last one, since magnetometer calibration is continuous and it takes samples all time not only when it asks you to position aircraft. That also means you can't put it anywhere close to metalic object (like roof of the car) until whole calibration is complete.
Avoid magnets or devices that may contain magnets (buzzer, gimbal etc..) they tend to saturate magnetometer such that it's showing just one thing and noise around that. External magnetometer must be far from the high current wires, metalic objects, magnets.