First, as noted above, there's the question of what you intend to do with these texts. Are you converting them for your own pleasure, or appropriating them for resale? If the latter, you've got bigger moral issues ahead of you than whether you add a few commas or not.
On the narrow comma issue, it seems to me that you have to assume that the usage of punctuation was a decision that the author either made or accepted. The work is by the author, not by you. It doesn't seem to me that you have much right to be tinkering with it beyond obvious typos.
Of course, if this is only for your personal pleasure, you should add punctuation in whatever amounts make you happy.
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