I don't have direct experience with mopar trigger wheels and sensors. I do have experience with the application of Hall sensors with targets. I do ground up ECU designs, including reference sensing, but I make what I want, and code to go with it. In your case the code is likely fixed, so the sensing means needs to replicate original signals in all respects.
The first thing, is capture cam, crank, and ignition primary signals on a logic analyzer along with timing measurement from timing light. That provides all necessary information to replicate, and properly setup.
Next thing is to accurately measure trigger wheel, and see how that compares to sensing signal. Typically widows shrink, because sensor triggers before and after tab, because sensor does not trigger at center point, it has diameter. Sensors vary in size too. Most Hall sensors sink current, go low with tab of target. Target should be anealed low carbon steel, not stainless.
