Can someone explain why this isn't Ar bhaca . . .? The question word for the past tense is Ar, not An, right?
There's six irregular verbs that use present tense forms of verbs: bí, feic, faigh, téigh, déan abair. So you'll see an, ní, sula and the present tense forms of the relative particles with those.
Not usually; for example, the pronunciations of aispeist have the first S slender in the Ulster and Connacht pronunciations, but broad in the Munster pronunciation. The eDIL shows that the Old Irish spellings of taispeánadh (found under taisbénad ) sometimes had the first S broad, e.g. tesbénad and tasfénad, so perhaps a broad pronunciation has existed as an alternative since those times.
The IPA transcript in the Myles Dillon/Donncha O Croinin shows a slender S (sh sound) used. Pronunciation was based on the Irish of West Muskerry.
Is "Have you seen..." translated differently? (I'm thinking of the song "An bhfaca tú mo Shéamaisín").
No - the Perfect tense in English is usually translated by the past tense in Irish (unless you want to indicate that it has very recently ended, when you might use the present tense and "tar éis").
The Perfect isn't explicitly covered by the Irish course on Duolingo, but it is mentioned in some discussions, (https://www.duolingo.com/comment/4347563) and there's a section on it in Gramadach na Gaeilge: