@tomek4: That Kindle is runing v 4.x.x firmware, right? For v5 firmware (Kindle Touch, Paperwhites, Voyage...) the location of hardcoded values is known, but IIRC nobody tried finding what .jar files on fw 4.x have margin values.
You would have to decompile jar files from your Kindle's system/main partition and search through Java bytecode until you find code concerning margins & footer/bottom progress bar.
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