Learn English – If something was vs If something were

The guiding principle should be don't use Past Perfect unless you really have to.

The uncertainty occurred after the asking - chronologically, and in the narrative sequence of OP's text. That's what normally happens when you report a series of events...

I did this. Then I did that.

It's grammatically possible, but completely pointless in most contexts, to express that as...

I had done this. Then I did that.

In OP's second example, it's pretty much impossible to avoid Present Perfect with the word must. You could get away with ...but it must be [that] you forgot..., but it's a bit "starchy". Present Perfect is perfectly natural here.

Consider, for example,...

1: You didn't answer the doorbell when I rang, so you must have gone to work early.
2: You didn't answer the doorbell when I rang, so you must have been in the shower.

Clearly in #1, the action in the present perfect clause (you going to work) happened before the simple past (I rang). But in #2, you being in the shower happened at the same time as I rang. That's not a problem in English; if the chronological relationship between actions is obvious from context, it doesn't always have to be made explicit by the verb forms.

Yes, this is acceptable.

Both your sentences present conditionals; although they are not expressed as formal IF ... THEN constructions, they might easily be so:

The situation would have been worse if he hadn't helped.
It would have caused us a lot of problems if anybody had not cooperated.

The protasis (IF clause) of a conditional may lie outside the sentence at hand; this does not invalidate the use of would:

It looked like the school might have to close. That would have been a shame. = If the school had had to close, it would have been a shame.

All of these uses are equally valid with non-past^✲ reference:

The situation would be worse without his help.
The lack of anybody's cooperation would cause us a lot of problems.
It looks like the school may have to close. That would be a shame.

In fact, most uses of would may be understood as implicitly conditional, though the actual condition implied may be very vague:

I would like a piece of pie. [eg, if you have any or if you would be so kind as to bring me one]
I would be happy to do that for you. [eg, if you were to ask me or if you need help]
I would never say such a thing! [eg, if the opportunity arose or even if I were provoked]

^✲ I should perhaps note that past modal + have + past participle , although it looks like a “perfect” construction, has nothing to do with the ordinary English “perfect”. It is, rather, the language’s workaround for the awkward fact that the modals can, may, shall, will may be used in their “past” forms with non-past (present or future) reference—which leaves them no convenient form for expressing the same modality with past reference. To accomplish that, we employ the “perfect” construction. It would have been is in effect the simple past of It would be.