Translation:Excuse me, are you going to the station now?
Yes, the same principle is behind perdone and perdona. The base verb is perdonar, do perdona is the tú form (same ending vowel), and perdone is the usted form (different ending vowel).
You can attach the pronoun me to either of these forms to make a literal "Pardon me". But unlike in English, adding the me is optional in Spanish.
Perdón is the noun, "(the) pardon" or "(the) excuse". You can use it just like the verb forms when asking for pardoning.
No, that's not correct in English. You can make a statement like "The store is now open", and you can even say "We are now going to San Diego". But you would not ask this question with "now" in that position. Putting "now" directly before the verb really emphasizes the "now", such as making an announcement that something that people have been waiting for is finally happening.
Also, why would you want to change the word order in the translation?
I don't agree that "Excuse me, are you now going to the station" should be accepted.
The fact that ahora/now is used should tell you to use the progressive here. No shade on anyone who speaks english as a second language, but that's immediately what I would think if I heard someone say "do you go to the station now". You could say something like "vas a la estación a menudo" to say "do you go to the station often" but if you're talking about now you should use the progressive.