Congrats, very nice and detailed evaluation.
I did look at the schematic but didn't notice the lack of decoupling caps on the VM supply.
Could you please check one more signal if possible, apparently you have the equipment and the knowledge for it ?
How long does it take for the TQ input to drop low after a step pulse is received?
I think that it will be short and will influence torque at low speed and this could create problems during acceleration.
Some machine setups might suffer from this, others might not.