I did not intend to be rude. I was just offering tips in response to "I hope this post is up to par". My apologies.

I'm not sure how I could have narrowed down the problem

Debugging is usually done by following the path the program takes and studying any deviations from the expected, and/or by examining the values of variables as the program progresses and studying any deviations from the expected. Data::Dumper should help you examine complex structures.

For example, you might have found that the array contained the wrong information after the while loop, so anything that gets executed afterwards is not relevant to the issue.

Proper programming techniques such as limiting the scope of your variables (you are currently only using global variables) and avoiding the use variables as variable names (such as ${pycvalues."$scalarcounter"}[2] instead of $pycvalues[$scalarcounter][2]) would greatly help you.