But it is out of appreciation and a desire to see how high you can go that I post this list of suggested dialogue edits! Note, these are only suggestions and you are free to note them as you see fit!
I've never seen someone compile an extensive list of suggested edits and then post them on a forum, but I have to acknowledge your good intentions--even if I question your expertise. To clarify:
Seeing as Dr. Bones appears to rely on parentheses to distinguish the MC's thoughts from the MC's spoken dialogue, even when self-directed or spoken for the player's benefit, you're correct to state that punctuation marks are included in the parenthetical sentences. These are functionally regular sentences enclosed by parentheses to distinguish them from regular speech, something that seems common in RPG games.
When using parentheses in general, however, I was always taught that periods were unnecessary when concluding one (because the parenthetical statement was
enclosed by parentheses) but that periods remained
outside them when ending the sentence (to indicate that
this is somehow distinct from it).
Also...the use of ellipses...in a sentence...tends to indicate...a pause. Especially when someone is speaking or something is happening gradually. I do think that spaces are unnecessary when the sentence is unbroken, but I don't know if that's a hard rule or just common practice. I've seen examples of both in many games.
I could very easily be wrong. I was always more concerned with diction, syntax, and the coherent progression of whatever I happened to be reading or writing than I was with grammatical minutiae, but in this instance I think you either misremembered a few things or I was confused by your summary.
Probably the latter...but since I'm mindlessly browsing with nothing better to do, I figured I'd throw my two cents in.