1. Manually test AFM wiper-track with voltmeter by moving flapper-door by hand slowly. Voltage should increase smoothly with no drop-outs. Should be around 0.75-0.85v at idle to 4.5v at max opening. If you find dead-spots, it may need bending the wiper-needle over to an unused area. I find it's easier to just slot the holes for the circuit-board and slide the board over.
2. test speed/reference sensors. Use oscilloscope and measure waveforms. Should match the following image.
3. also a good idea to go through each test in the DME/KLR Test Plan manual
in order. Some issues may point to a certain symptom & component, but the actual problem may be caused by something else up the chain.