I'd like to help on this, but without runnable sample code, and in the absence of visibility into the data structure in memory, it is difficult to devine what the issue might be.

Your code tends to use C-style loops, with parallel indices incrementing. This is somewhat error-prone. As an alternative, I'd suggest:

• Use idomatic perl style loops
• Use perl Classes/Objects as containers for these complex structures
• Give us a better idea of "what's wrong"
• Give us a better idea of what the objective is, and how this is supposed to work, and what the end result is expected to look like.

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