My impression is that punctuation is much less rules-based[*] in Japanese than it is in English – two authors might choose to punctuate the same sentence differently, especially with regard to whether they put in commas or not. If you would pause when speaking the sentence, you can throw in a comma if you like.
Question marks are generally for less formal writing, because in normal formal writing the questions are all か-marked anyway.
[*] Though you can certainly find blog posts online that are happy to list lots of rules…
I’ve also wondered before if punctuation has a stroke order, in particular 「」. One stroke or two, or does it even matter? I find they come out a lot neater if I write them in two but practice will probably fix that.