How do we know when to use 'it' versus 'he' in the translation of this sentence?
When it says "poorly" as a translation, does that mean poorly as in "ill"?
My guess is that it means "poorly" as in the adverb for bad: "go" is the "adverbial particle" which makes adjectives into adverbs, but "subjective" adjectives also take "go" (hence "bad" being "go dona"). I think?
Edit: I think I might be wrong actually. I don't know.
Given the lack of context, An bhfuil sé go dona? could have either meaning of “poorly”, e.g. “Is he ill?” or “Is it bad?”.
"Is he unwell?" is not accepted either, for what it's worth...
How is it possible that people have been pointing out the issue on this sentence and its lack of context/ambiguity for a year, yet it still seems to be broken?
You can't do much about the issue of context. But I would suggest that "Is he unwell?" isn't a good translation of this sentence. If you already knew that he was unwell, you could ask an bhfuil sé go dona to find out just how unwell he is, but if Joe didn't turn up for work today, and you wanted to know if he was ill or just off playing golf, you wouldn't ask an bhfuil sé go dona.
But go dona doesn't actually mean "unwell" or even "poorly" - go dona in a health context usually implies something more serious, just as you wouldn't ask "is it bad?" when the choice is between a hiccup or a sneeze. "Is it bad" tends to be used when you mean "Is it going to hurt a lot?" "Will there be a scar?" or "Am I going to die?" not when you mean "Does this mean that I won't feel like eating my dinner?"
(Yes, I know that you can have a "bad papercut", but that is usually reserved for one that bleeds a lot, or is going to sting).
You can do a job poorly, or badly, or not do it well and you would use go dona, but I think it might be a bit of a béarlachas to stretch that to "unwell".
Your second question highlights this - I don't think you'd ask an bhfuil tú go dona?, you'd say an bhfuil tú breoite or an bhfuil tú tinn?
Too bad we don't have context to know which of those two situations it would be. ;) But the other issue, aside from context, is what translations (for English) are acceptable for the word itself; I'd use "unwell" before "poorly", regardless of whether asking the question at all is appropriate.
To re-align a little bit, would it be better in second person? Is looking at someone in front of you and saying an bhfuil tú go dona more plausible?
Is bhfuil a form of bí similar to the habitual bíonn? Is what's being said here literally "Does it be poorly?"
No, fuil is just the dependent form of tá, eclipsed because it follows the interrogative particle an.