As a native speaker of English, from the UK, I would say that "I got there before the train left" sounds a bit better than "I got there before the train HAD left" ["arrived there" sounds just a little strange to me, but just "arrived" would be fine], but on the other hand "I got there after the train HAD left" sounds better than "I got there after the train left". But none of them sounds completely wrong to my ears - I think a native speaker might say any of those sentences! Not sure how helpful that is, but maybe it shows that you don't always have to worry about being too precise, whatever the grammar books say (though unfortunately in other situations you may just sound wrong if you're not precise - I don't know any way of predicting that apart from asking a native speaker).

I didn't get there until the train had left. (I got there after the train had left) - unusual. I got there before the train left.

When you want to say that something in the past happened after something else int he past, you put the second in HAD+Verb form. Most times that is a rule and will save you from making mistakes. I say 1st choice is correct

Yes, the first one is correct.

First is correct.