@olenesheim (I've edited your post to make it more readable)

From memory, the Troodon Vivedino doesn't come with a Duet3D mainboard, so I think you have a clone Duet board, and the official support that I can offer is limited. Also, from your config.g, you appear to be running RRF 2.x firmware, which makes it a bit harder to support you as we have mostly moved on to RRF 3.x now.

The best link I can find with information on the motor is here https://www.my3dtech.com/OMG/sst36c1080-motor/, and links to here for the manufacturers info https://jp.aspina-group.com/ja/products/motors/cat01/001/
It looks like the phases should be Brown/Orange and Red/Yellow, but it does seem that wiring and phases are correct from your tests.

So I'd think it's more likely a configuration problem. Looking at the motor specs, the only thing that jumps out at me is the phase inductance, which is 3.16mH. I think the inductance for your motor is 1.41mH. See here as to why inductance is important. This probably means you can't run it as fast as the old motor, and what you might be experiencing is that the step rate is too fast for the motor. What commands are you sending to the Extruder to test it? Your current settings are:

M566 E250 ; maximum instantaneous speed changes (mm/min) (jerk) M203 E3200 ; maximum speeds (mm/min) M201 E3200 ; accelerations

I would try halving all of these and test again. If that still doesn't work, reduce acceleration even more.

Ian