OK I have figured it out and i am going to leave this up in case it can help anyone else. One of my responsibilities at work is to manage a small CNC controls company we bought a few years ago. I have a PHD EE who designs boards on staff. I had him take a look and read the instructions. Here is where my mistake was that he found. In my experience Pin 1 is always next to the label. That is how you can look at a board and tell what end Pin 1 is on any header. On the programming header for the px1 Pin 1 is opposite from the label ( it is described correctly in the docs which is what I missed). So this entire time my problem was I was connecting the pickit3 backwards. At least now I can move forward.
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