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From what I understand, Japanese doesn't really have the concept of "swearing".
You can be rude by using words of inappropriate politeness.
(although I know there are games with language filters, including at least the later-gen Pokemon games)
It depends. First, do you know the hex encoding used for the characters? (E.g. If you open the ROM with a hex editor and find where the dialogue is, あ might be represented in hex by "4A", い might be "4B", and so forth).
If you do, you can at least do in-place editing. Change the hex code for each word/dialogue so that it spells out an English word instead. As long as it's the same size or smaller compared to the original Japanese, you can translate it that way. It's a pain though, haha.
If you also have the table file (basically a text file with the full set of あ = 4A, い = 4B rules in it), you might be able to use Atlas to automatically reinsert the script into the game. The script file you described sounds like an Atlas script, so you may be able to just run it that way.
Isn't that "No idea" image a school crossing sign?
Like this one: http://i.imgur.com/bjPTNok.jpg
English translation of things japanese is usually "dumb" in my opinion. So many games and anime (dont watch it but i've seen) just say things no natural english speaker would.
"so its YOU" no english speaker has ever used this as a greeting. FUCKING EVER,
"DON'T TELL ME..." god stop this one please
just mundane things that could greatly use a rephrase that any english speaker should feel awkward about saying.