Could have is saying that something was definitely possible in given circumstances.
Could have indicates that the option was available: that the possibility existed, not limited by circumstances, situation or personal ability. It tends to be used when you are talking about an entire hypothetical scenario.
When I was training for the marathon, I could easily have beaten you in a race!
The focus is on the capability: in this case the speaker knows that they definitely could have won the hypothetical race if such a race had occurred.
Note that saying they are definitely capable of doing so doesn't necessarily mean that it would definitely have happened, just that it had a probability of more than zero. A negative example might help to illustrate this:
Even if I had trained for a year, I could not have beaten Jesse Owens in a race.
It also doesn't give any indication of how likely the speaker thinks the possibility was, just that they believe it was definitely a possible outcome.
Would have defines a definite outcome given different circumstances.
Would have indicates that something intervened to stop the predicted outcome from arising. It tends to be used when you are talking about a change to the real sequence of events: if something had happened differently.
I would have beaten you in that race if I hadn't tripped up!
This is expressing certainty: if the situation was different (in this case, not tripping up), the predicted outcome (beating you) would definitely have occurred.
Might have defines a possible outcome given different circumstances.
Might have is the same as would have, but the speaker is less certain of the outcome.
I might have won that race if I had done more training.
I didn't win the race, I think I might have won if I'd done more training, but I also think that I still might not have won even if I had done more training.
Your specific examples
As you might have guessed, many of these sentences are correct but with subtle differences in nuance.
Example B
- If I hadn't been so tired, I might have realised what was happening.
- If I hadn't been so tired, I could have realised what was happening.
Because this is talking about a change from the actual situation, not an entire hypothetical scenario, "might" sounds more natural here than "could". That doesn't mean that "could" is wrong, just that it would be more common to say "might".
If you were sure that you would have realised what was happening if you'd been less tired, you could say "would" instead of "might".
Example E
- Why did you jump out of the window? You could have hurt yourself.
This is indicating that hurting yourself was definitely an option (and hence it was stupid to jump out of the window). For this reason, it expresses the sentiment most strongly out of all your "window" sentences. It's implied that you were lucky not to hurt yourself - in other words, luck was all that prevented you from hurting yourself.
- Why did you jump out of the window? You might have hurt yourself.
"I suppose you might have hurt yourself, but I'm not a window-jumping expert, so I don't know..." There's less certainty here, so it's less forceful. However, it's still entirely acceptable.
- Why did you jump out of the window? You would possibly have hurt yourself.
"Would possibly have" has the same meaning as "might have". To me, it sounds slightly less natural here, but I think that's because the question itself sounds a little accusatory, so adding the "possibly" in is a little awkward.
Example D
You didn't suggest a substitution for D but I'm including it to show the difference from E.
- I was so angry I could have killed her!
- I was so angry I might have killed her!
In this instance, it's actually the "might" example that is stronger. That's because the "could have" suggests that the speaker was angry enough to kill her, but chose not to. Because it's "could", we know it's a hypothetical scenario and that there was no chance of him actually killing her: just that his anger gave him the capability of doing so.
However, "might have" admits the possibility that this outcome might actually have occurred. It sounds like it's something external to the speaker that prevented it, like someone walking in, or maybe he went so far as to beat or shake her and it was only luck she didn't die.
Needless to say, "would have" is therefore the strongest of the three, indicating that she definitely would have died if something had been different (like they didn't get interrupted).
Example F
- I could have won the race if I hadn't fallen.
- I would possibly have won the race if I hadn't fallen.
These both sound equally natural, but the nuance is different. In the first one, the speaker is certain of their ability to win races, but acknowledges that that doesn't mean they'll win every race they ever run. Falling stopped them being able to win the race - an ability they had before they fell.
In the second sentence, on the other hand, the speaker is still acknowledging that the outcome of the race (even without falling) was uncertain, but they are doing it in a way that includes the possibility they might not have won the race because they simply weren't good enough. It's a broader statement: that they might have gone on to win if they hadn't fallen, but they don't know if they would have gone on to win.
Some other things you mentioned in comments
I think your would possibly/perhaps have example is the same as might have, and would have been able to is the same as could have, with would have been allowed to being a subset of that where permission is the limiting factor of the "could".
Best Answer
Not sure if this is exactly what you want to understand. I didn't read through the other posts. Solely going by the examples you gave:
There is still a condition that needs to be met in both instances.
First example, it is uncertain that the guy whose fingerprints they found is the actual burglar. He hasn't been formally convicted of the crime. Therefore, he is still only a suspect until further investigation and prosecution.
"Why did he steal the money?" Means that he did steal it but they want to know the reason.
"Why would he have stolen the money?" Means they want to know the reason this person (provided he is the culprit) wanted to steal it (possibly to use this as evidence in a prosecution.)
Second example, I can't pinpoint because I don't recall this passage but it seems that it's possible someone else investigated and B didn't get the opportunity or something to this same effect. B somehow didn't meet a certain condition in order to actually investigate but you can't make the claim that he actually investigated.
Your sentences are grammatically correct but they don't fit because they conclude that something has happened. The thing is, we don't know for a fact that it did happen.
Hope this helps some.
EDIT: I just read the other posts. Aside from what has already been stated in the other post about 'expression of disbelief'. It is also a matter of intonation, emphasis and context.
Consider this:
/Why would he steal my money?/ - uncertain if he is the culprit
/Why would HE steal MY money?/ - uncertain and stressing ownership
/WHY would HE steal my money?/ - disbelief that 'he' is the culprit
Although all three are written the same way, from a written dialog it would need to be deciphered by context. In a spoken dialog, it would be deciphered by tone and emphasis (and context.)