What am I doing wrong? (Alignment)

What am I doing wrong? (Alignment)

So, I am attaching some photos that I took to better explain where I'm at with this obstacle I'm facing. I followed the many steps that I received through the community here, and the YouTube videos provided and after trying them out myself, (please look at the photos) I am running into the issue of having to align my part manually AGAIN! 
  1. my set up (As you can see, the fixture is pinned down into the able)
  2. program sequence
  3. Prompt
  4. Measuring slot after clicking "No"
  5. probe compensation cannot be applied (which happens for every single feature hereafter, resulting in parts out of tolerance, when really they're not)
Maybe its the alignment I'm using. What better way to tackle this? Thanks!