In O que preciso fazer the “e” in que sounds as I would expect, like “u” in the English word nut. In O que achas it almost sounds like the English word key. Am I mishearing? Is there a rule or general pattern to explain this? Or does this vary by speaker or region?
Olá, @fitterman, welcome. You’re not mishearing, that’s accurate 
It’s not that the pronunciation is officially different in each case, but in practice, some vowel sounds are modified when the following word also starts with a vowel. That’s the case here, where the ending E in “que” is modified by the starting A in “achas” and sounds more like the English ‘ee’ sound.
These little modifications actually make things easier for us in regular/fast speech, which is why we do it all the time!
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Obrigado @Joseph, I’m glad to hear there’s some logic to this! There are two more questions that this sparks. First, is there a set of common cases where the following word determines something about the pronunciation of the previous word? French has “liasion” to describe a similar situation in that language. Do you have a name for this in Portuguese?
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Sorry, @fitterman, almost forgot to get back to you! 
There are just a few, at least that I can think of right now. But note that none of these are mandatory, especially since we can simply just drop the first vowel. So, you may not always hear these “liaisons” even when they’re possible. Also: 1) I’m basing this mainly on the pronunciation patterns I hear around me and use myself, in Lisbon + surroundings; 2) check out the interactive table at the end of this article for sound references of each vowel type (closed, medium, open):
Unstressed ending E vowels followed by medium or open vowels E, A or O → These will be closed E vowels, which may sound like the English e when followed by the aforementioned vowels. I’d say this happens more with monosyllabic words like que, de or se, or enclitic pronouns like -te or -me, than with longer words.
-
O que é que achas? (What do you think) → O qu[ee] é que achas? (modified first vowel) or O qu’é que achas? (omitted first vowel)
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Tu és de onde? (Where are you from) → Tu és d[ee] onde? (modified first vowel) or Tu és donde? (omitted first vowel, which forms a contraction in this case)
-
Eu quero-te aqui (I want you here) → Eu quero-t[ee] aqui (modified first vowel) or Eu quero-t’aqui (omitted first vowel)
Unstressed ending A vowels followed by medium vowels A or O → These will be medium As, which tend to be omitted themselves and also change the following vowel into its open version. This may happen with any word in general, not just short ones:
– Medium A + medium A = merge into one open A
- É a avó! (It’s grandma) → É [à]vó! (open A)
– Medium A + medium O = merge into one open O
- Paga o que deves. (Pay what you owe) → Pag[ó] que deves. (open O)
Ending S consonants followed by any vowel sound → These tend to go from a sh sound to a zz sound, as is usually the case anytime the letter S is between vowels. The letter S is explained in detail in this Learning Note (The Letters S and C) and in this other forum topic (How to pronounce "s" at the end of a word).
- Os homens são altos. (The men are tall) → O[z] homens são altos (note that the letter H is always mute, so the vowel sound after it is all that matters)
We don’t, or at least we don’t have any layman’s term for it.
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