I have some rather tricky file manipulation I need to perform, but I am rather bad with coding and I am immediately stumped with where to even begin. Any help would be amazing, so thanks in advance. Preferably in Shell or Python as they are the languages I have cursory knowledge of, however if there is an easy solution in another language I am open to it.
You will need to learn Python better than you know it now. Here is an outline what you will need to do. It is very typical for this kind of "file manipulation".
file2(or two regular expression if the files do not have the same format). Include in your regex, syntax to capture groups that are important to you.
file1line by line.
file2line by line.