One thing you could try is opening the file in the Desktop FBReader. This will at least tell you what format and encoding FBReader thinks the file is using. You can also try other encodings (and fonts) to confirm that the problem can be fixed.
Note that there are two potential reasons for "boxes" in FBReader, the encoding could be wrongly selected or the font could be missing the needed symbols. If you are getting random bad characters (vs boxes), then it is almost certainly the encoding. Similarly, if the ePub version is working then it can't be the font and must be the encoding. Note the encoding isn't "English", it is probably windows-1252 or UTF-8.
If you can get SSH over USB working (possible from a Linux Desktop) then access to the books.xml is relatively easy, otherwise it isn't.
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