***Not a teacher***
Wow, what a detailed/subtle set of questions! I'm no expert, but here are my thoughts on the examples you cited:
First example: Both sound good, though the recency of the book-reading is clearly different. And "what have you done today?" is a fine question, though given a certain intonation it could perhaps put people on the defensive. Not sure why- maybe it is the aspect of completion. So what have you accomplished, anyway? :)
Second example: just as you said, the simple past implies completion. Combined with "just" it implies recency and completion, which starts to sound like it wasn't a very careful examination. "Just finished looking over" takes away that problem. "Have been looking over" is also good, with an implied open-endedness.
Third example: "Who have you talked to?" seems to imply something developing or ongoing. So you have a terminal illness- who have you talked to (to get advice)? You saw something you weren't supposed to- who have you talked to? Who have you been talking to- this could mean the same things as above. But it could be a general question, implying regularity.
Fourth example: Not really sure, but the first sounds much more common.
Fifth example: I have no additional information apart from what is in example three, but I can say that the middle phrase, "why have you talked to him?", seems pretty uncommon.
I hope that is at least a little helpful.
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