To do at least some of what you require you need to save the document as a template (see attached) and create new documents from it, otherwise automating from a save event will make an unholy mess of the original.
When you first save the created document it will copy the table to the start as requested, leaving the original in situ.
Because of the way you have formatted the document, if you hide the check boxes, the general format of the document is lost as space changes to accommodate the hidden controls. This is a particular issue with the tables that has no simple answer.
If you really must have the various unchecked options hidden, I wouldn't have them in the document in the first place. I would instead employ a userform -
Create a userform to make the selections and write the appropriate entries to content controls, but that would mean a complete redesign and a steep learning curve to create the form.
If that is too onerous, I would suggest not attempting to hide them. In addition to the formatting problems you will encounter, unless you submit the form as PDF, hidden texts are easily unhidden, which rather defeats the point of hiding them.