I've found it's helpful to find the letters or letter combinations in the words you find most difficult and practice them separately from the rest of the word. For example, ferrocarril . I found it difficult at first to pronounce it all at once. I chopped it in half and practiced until I could say ferro and carril independent of one another, then tried to properly pronounce them as one.
For making the pronunciation of Spanish letters and words become more natural, I try to recite the alphabet in Spanish regularly. (My advice, don't stop until you feel like a child reciting their ABCs all over again. ;) )
Best of luck!