"Dlaczego" and "Czemu" mean exactly the same thing. Some people may find "czemu" slightly colloquial and a bit 'worse', because it may be considered a Russicism.

This is normal past tense, pluperfect is pretty dead nowadays (apart from "powinien był", the past of "should"). Both of your versions work, but I agree the 'had' part looks kinda strange, so I'll go with "have" as the default one.

This is present tense, as opposed to the past tense in the Polish sentence.

Never mind, I see my mistake.