Yes so I’ve done that, reassigned the motor outputs from 1-4 to 5-8 and went for a short test flight in ALT hold, it went fine, here’s the log:
I’m not sure where to find the RPM in the log viewer, is it the same as this?
Change the outputs to 9-12 (Aux outputs as stated).
I’m using the cube mini carrier board which exposes only1-8 output channels pins, is there a way to remap the pins for different channels?
Not True. The FMU pins are the AUX outputs. Change them and then update the Bdmask parameter to reflect it.
Oh thanks for pointing this out, I’m learning alot here, I’ll reconfigure, rewire and go for another test flight
After connecting in Mission Planner look on the messages screen for the RCout message. It will tell you what the channel output protocol is. If you don’t see Dshot something is wrong.
In the message tab it looks fine:
RCOut: PWM:1-8 DS600:9-12 PWM:13-14
I went for a test flight and here’s the log
Well done, you now have Dshot on 9-12 and you have ESC RPM showing in the log. We can circle back on the serial telemetry which isn’t present. But 1st let’s re-configure the notch filter and advance to an Auto Tune.
You didn’t make these changes:
ATC_ANG_PIT_P,9.0
ATC_ANG_RLL_P,9.0
PSC_ACCZ_I,0.34
PSC_ACCZ_P,0.17
Make these changes and don’t miss any parameters like Loop Rate:
And change this:
SERVO_DSHOT_RATE,2
Note: You have Serial5 protocol set to 16. If you have connected the ESC to Serial4 then fix that.
Also: Looks like the quad is front heavy. Can you move the battery back a bit?
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I’ve set up all of the above and went for a test flight, I don’t know if what we’ve done so far makes much of a difference but I already feel like it flies much better 
Do we have to further tune the notch filter or we can proceed to the next step?
BLHeli still can’t read my ESCs and I’m not really sure why I need to flash the ESCs, what purpose it serves? I saw that you can set up your ESCs in many different ways, reverse them and so on, but not sure what it helps me with
Yes it is front heavy right now, I’ll have to deal with this somehow later I hope it doesn’t affect this process, I’ll try moving the battery a little to the back for now
Here’s the log of the test flight, in ALT hold and LOITER
Thank you so much again for the help, I really appreciate it, you’ve helped me alot 