1. Open your pdf with Adobe Acrobat Pro.
2. Click Tools >> Pages >> Crop
Set margins and crop document. You can use different page range, odd and event page settings.
3. Once you cropped your file Click Tools >> Protection >> Remove hidden information.
4. You will see Status: Finding hidden information, then Results . Once all the hidden information found, you can check/uncheck each group of information.
5. Click Remove.
6. Save your document. You have removed page numbers and headers and other information that you cropped out, permanently.
Note: Dropping cropped pdf into Calibre directly may not yield good results. Especially if you have unicode characters on your pdf. Better option, first convert it html first.
7. Now, lets save our pdf as html before converting it into mobi or epub document. Click File >> Save As >> More Options >> Html Web Page
If you cant save your file as html, make sure you unchecked "Run OCR if needed". For that, click "Settings" on "Save As" screen.
You can do some manual fix befor conversion if you like.
8. Drag and drop html file into Calibre, and set TOC and other stuff and convert.