I've taken a preliminary look.
I know that it may seem redundant, but questions here are answered by volunteers. Please do not make them download and review a document to see if the questions are ones they can help with. Please edit your original post to at least give more of an idea of what the nature of the problems is.
I've attached your original "template" with some changes. Please take a look at it.
In
Word jargon, this is NOT a template, but a document. The distinction is important.
Using the term "template" will lead you to very different information online and in Microsoft's help system. (Yes, it is a template in the ordinary English-language sense.)
Templates in Microsoft Word
More jargon: You use the term "header" when you mean "heading."
What is the difference between headings and headers?
I replaced the Cover Page with one of the stock pages from the Cover Pages Gallery. You can reformat it as you wish. The thing is, it ends up as Page 0.
The first section's headers have been set to have a
Different First Page, with page numbering starting in the regular or primary header.
Header/Footer Settings Recap
I restarted page numbering at 1 in the second section using the Format Page Numbers dialog.
Issue 2 - Labels not wanted in List of Figures as in the List of Tables
I cannot figure out how you accomplished this in the List of Tables.
While I can think of ways these could be removed it is not simple and will make editing and maintenance of your documents a chore.
These are TOC fields with switches. Each caption will need to be massaged to get this result. Here is my writing on these:
Insert a Table of Figures. See also:
TOC Switches by Suzanne Barnhill, MVP
Your List of Tables field that includes the Table numbers but not the label is:
{ TOC \h \z \t "Table,1" \c "Table" }
I tried using the identical construction for the List of Figures but the labels still appear.
I note that you are using the List Paragraph style for the headings on your List of Figures and List of Tables. This is a very strained usage. Consider instead using the TOC Heading Style. Perhaps a Custom TOF Heading Style based on the built-in TOC Heading Style but with an Outline level of 1 applied.