Hi Jason,
It seems like the amplitude of phase current is oscillating. Can you tune the T control Advance setting and make sure that there is not much oscillation in amplitude.
You are right on motor parameters, as motor is running for longer time it will get hot and motor parameters start drifting from the value measured at room temperature. It will be good to configure parameters measured at higher temperature.
Another change I would like to suggest is changing deadtime 360-400 nS.
Let me know if changing the parameters help.
Regards,
Krushal