Now that is a very bad sentence. It's true that a lot of 'had's can (and should) be eliminated by simply changing the sentence structure. In the case of the sentence above, I'd cut half of it and just write, 'John and Raven had met in the third grade and become instant besties,' for instance. It can also be a good idea to restructure or rephrase sentences with 'was' in them. A good way to make things more interesting. Either way, though, the key is variety. If every sentence in a paragraph is 'subject, verb, object', things get boring fast, for instance.
While punctuation definitely counts, punctuation rules in English are actually extremely complex, convoluted, and inconsistent, especially where commas are concerned. There are vast varieties of styles that use commas differently (Oxford comma or not is only one of many points where people wildly disagree) and no hardcore rules for them. You can ask three different editors who are equally experienced, educated, and knowledgeable and get three completely different answers about comma placement.