When 'past modal+have+past participle' accompanies with past tense in a sentence, can it be before the past or at the past?

Question

Hermione, however, had more on her mind than the Sorcerer's Stone. She had started drawing up study schedules and colorcoding all her notes. Harry and Ron wouldn't have minded,[A1] but she kept nagging [B1] them to do the same.
"Hermione, the exams are ages away."
(Harry Potter and the Sorcerer's Stone)

"So you mean the Stone's only safe as long as Quirrell stands up to Snape?" said Hermione in alarm.
"It'll be gone by next Tuesday," said [B2’] Ron.
Quirrell, however, must have been braver [A2] than they'd thought.[B2] In the weeks that followed he did seem to be getting paler and thinner, but it didn't look as though he'd cracked yet.
(Harry Potter and the Sorcerer's Stone)

She could have wept [A3] It was bad, it was bad, it was infinitely bad! She could have done it differently of course; the colour could have been thinned and faded; the shapes etherealised; that was [B3] how Paunceforte would have seen [A3'] it. But then she did not see it like that. She saw the colour burning on a framework of steel; the light of a butterfly's wing lying upon the arches of a cathedral. Of all that only a few random marks scrawled upon the canvas remained. And it would never be seen; never be hung even, and there was Mr. Tansley whispering in her ear, "Women can't paint, women can't write ..." (Virginia Woolf, To the Lighthouse)

For Cam grazed the easel by an inch; she would not stop for Mr. Bankes and Lily Briscoe; though Mr. Bankes, who would have liked [A4] a daughter of his own, held out [B4] his hand; she would not stop for her father, whom she grazed also by an inch; nor for her mother, who called "Cam! I want you a moment!" (Virginia Woolf, To the Lighthouse)

I guess the tenses are like these. Which one needs to be corrected?

A1 : before Speech Time, at B1
A2 : before Speech Time, after B2, at B2’
(A2: at B2; ‘must have been’ generally coincide with the past but in this case with the past perfect?)
A3 : at B3
A3’: before B3
A4 : at B4

Answer 1

You've pretty nearly nailed it.

In all of these, [past-form modal] + have + [past participle] may be parsed as the 'simple past' of [past-form modal].

If you "foreshift" them all into present direct speech, where Reference Time coincides with Speech Time, all your [A]s become past forms and all but one of your [B]s become present forms. I've relabeled the exception as [C2] and given you a new [B2] later in the passage:

1. "We wouldn't^A1 mind, but Hermione keeps^B1 nagging us... "
2. "It'll be gone in a week" says^B2′ Ron. ... a week later:
   "Quirrell must^A2 be braver than we thought^C2. He does^B2n't look like he's cracked yet."
3. "I could^A3 weep. It's bad, it's infinitely bad ... that is^B3 how Paunceforte would^A3′ see it."
4. "Though Mr. Bankes, who would^A4 like a daughter of his own, is holding^B4 out his hand, I won't stop for him."

Than they'd thought in #2 is, as you observe, a true past perfect, lying to the past of Reference Time, and is consequently foreshifted as a past form. Reference Time for this sentence is the time in the following weeks when Quirrell fails to crack. In fact, your [B2], my [C2], coincides with [B2′], when Ron expressed the thought that Quirrell was not brave enough to stand up to Snape.