[MPaulHolmes]

The PI ratio was just a variable that was there for when the "auto" PI test was running. It gave a starting point for how to check a bunch of values. So, if you had the PI ratio be 100, the "run-pi-test" would do:
Kp = 100
Ki =1

Kp = 200
Ki = 2
.....

but it doesn't come into play when you are independently setting Kp and Ki. So, let's say you did this:

pi-ratio 50
kp 1000
ki 10

the variable named "pi-ratio" would still be 50, even though now Kp / Ki = 100.

The rotor time constant can vary a lot from one motor to another. The motor will run horribly if you are way off. It will run OK if you are a little off, and it will run the best if it's perfect. The "run-rotor-test" only works on an unloaded motor. I"ve only ever tested it on a bench with no transmission. If a transmission is hooked up, you man need to change the default commanded Id and Iq in the rotor test function "RunRotorTest" from
IdRefRef = 300
IqRefRef = 300
To something bigger. Those numbers just worked OK for me on a bench with a unloaded motor at maybe 60v or whatever it was I was using for the test.

If you can't get the run-rotor-test to work, you can just try guesses from 5 up to 150 (5mS up to 150mS for the rotor time constant):

rotor-time-constant 5
rotor-time-constant 6
...
rotor-time-constant 150


and see what gives the best acceleration.

Arber, does your ABZ encoder have a single index pulse per mechanical revolution, or is it 4 per mechanical revolution? That's the only difference from motor type 2 to motor type 3. One possibility is your encoder doesn't like one of the settings below:

		case PERMANENT_MAGNET_MOTOR_WITH_ENCODER:
			QEICONbits.QEIM = 0b110; 	// enable QEI x4 mode with position counter reset by INDEX pulse. 
			QEICONbits.PCDOUT = 1; 	 	// Position Counter Direction Status Output Enable (QEI logic controls state of I/O pin)
			QEICONbits.POSRES = 1;		// Position counter is reset by index pulse.	
			QEICONbits.SWPAB = savedValues2.swapAB;		// don't swap QEA and QEB inputs.  
	
			DFLTCONbits.CEID = 1; 		// Interrupts due to position count errors disabled
			DFLTCONbits.QEOUT = 1; 		// Digital filter outputs enabled.  QEA, QEB. 0 means normal pin operation.
			DFLTCONbits.QECK = 0b011; 	// clock prescaler of 16. So, QEA or QEB must be high or low for a time of 16*3 Tcy's. 
										// Fcy = 30MHz.  3*16Tcy is the minimum pulse width required for QEA or QEB to change from high to low or low to high.
										// You can do at most 30,000,000/(3*16) = ??? of those pulses per second.  So, you can have at most
										// ??? * 2 clock counts per second, since resolution has been multiplied by 2 (QEA and QEB up and down transitions all cause a pulse to be seen by the microcontroller..)  
										// 
			DFLTCONbits.IMV = 0b00;  	// INDEX pulse MUST happen when QEA & QEB is low. It didn't work for QEA being low with the Leaf motor.
			MAXCNT = (savedValues2.encoderTicks << 2) - 1; 		// If going backwards, poscnt will go from 0 to maxcnt, ONLY IF it is caused by an index pulse!!!  Multiply by 4 since I"m doing 4* the resolution.
								// Use this for the AC controller.  It's easier to measure speed of rotor with this setting, if there's no INDEX signal on the encoder.
			POSCNT = 15000;  	// It starts in an unknown state before the index pulse happens. Do this so I can know the index pulse hasn't happened yet.  It will vary from 14000 up to 16000 or whatever, and suddenly be forever trapped in [0,MAX_CNT] once the index pulse happens.
			myFirstEncoderIndexPulseTest.startTime = 0;
			myFirstEncoderIndexPulseTest.currentAngleOffset = 0;
			myFirstEncoderIndexPulseTest.testRunning = 1;
//			encoderTicksDivPolePairs = __builtin_divsd((long int)savedValues2.encoderTicks,(int)savedValues2.numberOfPolePairs);
		break;

I would try changing "DFLTCONbits.IMV = 0b00;" to
"DFLTCONbits.IMV = 0b01;", or DFLTCONbits.IMV = 0b10;, or DFLTCONbits.IMV = 0b11;
Those are the possible required states of A and B, when the index pulse happens, and I don't know what state A and B are in when the index pulse happens on your encoder, so you would just have to try them all. This is why companies pick a specific motor and specific position sensor and just make a specific controller for it. Everybody has their own standards.