The numbers in the margin is a setting on the device. In the Reading Setting page, uncheck the "Show Adobe EPUB page numbers" option. By default, it is on, so you must have unchecked it on the Clara HD.
But, the difference in font sizes suggests you have disabled or removed the KoboTouchExtended driver. Using that would have sent the books as kepubs. The font scaling is different for kepubs than epubs. For the same setting, the font in a kepub will appear smaller than in an epub. Plus, kepubs never show the page number in the margins.
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