Word BY word emphasizes the 'one at a time' nature of the action. Word FOR word puts the focus on the exact or literal nature of the translation. The difference might show up in some situations. For example, if someone has to say something very slowly, perhaps for a dictation, it would be done word BY word. If you are repeating a piece of gossip you have just heard, you would not do it word by word but word FOR word. Well, you would do it word FOR word if your memory was good! Word for word implies verbatim/exactly the same words/exactly the same meaning/accurate. "Susie told me what Harry had said, word for word!" (Susie repeated Harry's words accurately.") You would not substitute 'by' into that sentence about Susie and Harry. Word by word implies one at a time. "Our lawyers examined the contract word by word, clause by clause, sentence by sentence, to check it was correct." (You would not substitute 'for' into the sentence here).

To me, they mean the same thing.