It's really hard to make literal traduction when it comes to songs, poetry, or even sometimes comedy stuff. There can be a lot of metaphors/word plays. My native language isn't english either.
The face on the clock = I guess seeing your face aging ? Or it's time to go to work. The ship is just a frame = a ship is a boat. Wether the ship is his life journey or his means of escape...I think "just a frame" is a way to distance himself from whatever is going on. "Your foreign body" just before could be about this as well.
Seething decks = hard to say. It could be about getting to work on the "ship" , and there's lots of activities. I think seething is often about boiling water or anger so it's not really something joyful.
Hands beyond hands ...= could be about rowing the ship.
I guess the somewhat literal meaning, is the person leave his family/problem behind and go on a ship to who knows where (probably hell ), he's in bad shape, and just row mindlessly away. Trying to distance himself from his past, and even his own body.