So for an update to my above problem. I found when running without AccelStepper (just looping stp pins from HIGH to LOW), I will get similar behavior when I put a significant delay after setting the LOW stp pin. Setting this to delay(4) or greater starts to make the motor run very loud and with heavy vibrations.
So my current thinking is AccelStepper is currently set to run with a longer delay here as well? Although it seems odd other people would have similar problems if this was the case...
The below runs smooth
digitalWrite(dir, HIGH);
digitalWrite(MS1, HIGH);
digitalWrite(MS2, LOW);