Paneling Tools problem with panel results

I am having some trouble with Paneling Tools.

Firstly, I am having two results which are undesirable and I have not seen in any of the tutorials a reason for this kind of problem. You can see in the below two images, 1) there is an area of my shape which is left incomplete. 2) The Paneling Tools is creating geometry through the center of my shape. This is also not what is desired.

Another thing I am trying to understand if it is possible, but also how to accomplish-- Once I get my two problems solved with this shape, I would like to understand how to make random cuts throughout the shape. Below I am attaching an image of what it would look like if I were be using a BooleanDifference to accomplish this. As an example, I would like to use all the gray shapes as my cutting tool to make the cutouts in the green panels. The obvious problem with doing just this is that none of the cuts will be truly planar to the panels, and the Boolean functions will likely fail without quite a bit of work to get them just right on each panel. Also, as mentioned, this wouldn’t be random in such case:

Please HELP! And thank you in advance for any help!

For the first problem, you need to wrap the grid. An example is shown on page 12 of this guide:

(the guide is for GH, but the wrap grid concept is the same and can be found in Paneling Tools->Grid utility-> Close or Wrap Grid
as for the rest of your question, you may want to upload a model.