Beginner Help with Multiple Alignments

Its hard for me to post my code because my CMM has to run independent of our network due to some overly complex security protocols here. But, based on the response, I can "leap frog" a new alignment (A3) based on geometry I have created within the previous alignment (A2)? As long as that is a true statement, I will spend the time to find my mistake. I probably selected the wrong feature when defining my A3. Thanks for the confirmation.

I would not leapfrog on a CMM if the part fits within the volume of the machine. 
It sounds like there is an error in your alignments or a bad hit somewhere. 
Try doing it again, 3 hits for a plane, 4 hits for each circle, create a line between the circles. Do your first alignment as...
Level plane to Z
Set Z origin to plane
Set XY origin to one of the circles
Rotate X or Y to the line (whichever is appropriate for your setup)

Once that is done, assuming your using a Hexagon machine with a NextJogBox, hit the button to change to "part" coordinates and slowly move the probe around and see if its following your parts direction. If you move between the dowel holes your machine should move in a straight line in whichever axis your rotated to.

I would not leapfrog on a CMM if the part fits within the volume of the machine. 
It sounds like there is an error in your alignments or a bad hit somewhere. 
Try doing it again, 3 hits for a plane, 4 hits for each circle, create a line between the circles. Do your first alignment as...
Level plane to Z
Set Z origin to plane
Set XY origin to one of the circles
Rotate X or Y to the line (whichever is appropriate for your setup)

Once that is done, assuming your using a Hexagon machine with a NextJogBox, hit the button to change to "part" coordinates and slowly move the probe around and see if its following your parts direction. If you move between the dowel holes your machine should move in a straight line in whichever axis your rotated to.