You can use the crop tool to set all pages to the same size. Let's say most your pages are all about letter sized, with some being a bit smaller. You can then use the Crop or Set Page Boxes tool (Tools>Organize Pages>Set Page Boxes in Acrobat DC or Tools>Pages>Crop in Acrobat XI) to adjust the page sizes:
Just select a page size (you cannot make the pages smaller using this function, that would be done by setting the crop box in the upper part of the dialog), select to apply to all pages.
Karl Heinz Kremer
PDF Acrobatics Without a Net
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