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Most curious.
Would probably need to see the original mobi (that doesn't exhibit the whitespace issue) to see where the extra whitespace might come from (or a small mobi that exhibits the same behavior if the one you're using is too large and/or copyrighted).
You might try immediately rebuilding the html with Kindlegen (untouched by Word) to see if the unwanted whitespace is still showing up.
If I had to guess, I'd say using Word to do your splitting is where the whitespace gets introduced--regardless of what viewing the html in calibre shows (the test suggested above should confirm that). I'd recommend using Sigil or just a plain text editor of some kind to do the actual HTML editing/splitting. Nothing wrong with Word if it's all you have/know, but it's going to take liberties with the code.
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