Derek,
I'm a little confused as to why your custom board is setup to sense 400A of current. What is the maximum current you expect to use with your motor? The reason I'm concerned about this is the finite ADC resolution. If you only ever expect to run with 37.5A, but you can sense 400A, you are only using 8 of the 11 bits (one is lost to sign) of resolution on the ADC. This will impact how well you can control the motor.
But the motor parameter identification can be treated as a separate issue. When the motor parameter identification runs, it needs to control the current in the motor, but without knowing the motor parameters it needs to be de-tuned to the point where it will still work. So it assumes a very slow tuning, and attempts to control the current in the motor. Under some situations this may not work.
Also if you are switching 400A, what is the PWM frequency you are using. Most IPMs that can handle that much current can't switch very quickly, and if you motor is too small the inductors act like wire instead of inductors, making control impossible.
Where you able to estimate the motor parameters and spin the motor using the reference hardware? If so, you shouldn't need to perform the motor parameter identification on your custom hardware.