You can save as filtered text, but clean the stuff up first!
Anyway, from a quick glance you could replace the margin in the .calibre16 class and replace it by margin-top: 4em; or something like that.
It is difficult to say with a calibre conversion like this due to the naming of the classes combined with the Word HTML garbage.
I strongly recommend my add-in. Not only for the creation of the ePUB, but also for the other procedures to improve the source document.
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