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.)
Congratulations! You understand this too well to be intimidated by a textbook.
As it stands, the last sentence in ONE is probably in error; on the 'default' assumption that its reference is to Ann's current obligation, it should read
A: It's 7.20 and Ann is sleeping.
B: She shouldn't be sleeping. She should be getting dressed.
However: if the sentence made an explicit reference to a past time, it would not be in error:
She should have been getting dressed twenty minutes ago.
Best Answer
I have seldom come across the phrase make sure taking any other form of a verb. It has been always the base verb.