For Starters, Japanese is *_very_* contextual.
So the only context where I could think of "iki masu ka?" being on its own would be in a conversation dealing with person asking about if person x left already or not...
Now in the sentence you specify it can be thought of differently... (remember, A LOT of the time things can not be translated directly between languages and ESPECIALLY with Western vs. Eastern languages.)
Sumimasen in this sentence would be excuse me.
Kyoto-eki = Kyoto Train station
wa is just the particle making Kyoto Train Station the subject of the sentence.
douyatte = by what means
ikimasu = "to go" in the polite form
ka is the particle making all of the above into a question.
Knowing that we have:
"Excuse me, Kyoto train station (<-Subject) by what means to go (<-Question)"
Now, if a Japanese person who knew very little English came up to you and said "Excuse me, Kyoto train station by what means to go?"
You would think at first "Wow that guy's grammar sucks..." because we are all grammar Nazis as native English speakers.
Then you'd probably move on and think (or say) "You mean 'Excuse me, How do I get to Kyoto train station?' right?"
That is how you get the translation of that sentence.
This sentence is probably going to be one of the easier ones that you will have to translate in your head, that is until you become adjusted to thinking in a Japanese style.
My main point is that Japanese is an *_Idea Oriented_* language and Romance Languages (like english) are more Syntax Based which is why most of the time if you translate strictly between Romance Languages (Spanish, French, English etc.) you will do pretty well.
So in other words, don't think of 行く (iku) as "to go" think more about how "行く" is the general concept of going from place to place?
Do you get what I mean?