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I can feel a little bit of what you are trying to do but the immediate problems make it very difficult to understand the goal. For example, you are using arrayjob while having the excellent pgfplotstable naturally supporting pgfplots . You have a few macro names with numbers, overwriting definitions ...

Where would you put those cones with respect to the nodes? You can also consider drawing dashed lines (a web-like structure) in the background to indicate that there is more to the graph than it is already being shown.

You might better avoid the nesting of arrays as much as you can in order to avoid such spacing and padding problems.

Here is something that comes to close to the given example. You can still modify the array stretch to 1.3 or higher, alternatively add some \mathstrut s etc. I recommend reading ...