So Paul decided to help me further with my frustrations on the algorithm, it simply does not work. I attempt to debug my code with something visual I can wrap my head around. I zealously take screen shots to determine where the problem lies after each one dollar comparison step. I finally figure out that my whole process of grabbing points is wrong. I reformat my zeros and ones to point by point, being in a time sequence in which they are entered. This fixes the problem but only after I dumb down the scoring algorithm even further and add and point by point difference and then sum then up. What I mean by point by point difference is taking the euclidean distance between the two points. I pretty much remove the rotation step and the angular stuff for scoring and all is well. Paul was very helpful in helping me troubleshoot this issue. Here are some screenshots of my JFrame output of the points during each step. To simplify things I ended up creating a separate Java Application with a JFrame with some database and input dummy data for testing.

The resampling (you can see here this is bad, the old way was putting points in in top left order instead of time order)

The rotation, things get weird here

The translating the origin and bounding, this parts fine
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