Recently I cropped pdfs so that they would be larger when I viewed them in the Kindle DX. I did not convert them into a mobi file. I just wanted the pdf as is (an image basically). When I cropped my pdf using Adobe Acrobat reader and saved it, I noticed that when I viewed it in the Kindle the cropped did not apply to the pdf and it appeared in the original format. So how did I save my cropped pdfs so that they appeared the way I wanted them (cropped) on The Kindle? Simple. I exported them as pngs and then recreated the pdf using the pngs I exported from the cropped pdf. Here’s the steps:
1. Go to Tools–> Advanced Editing–> Crop tool
2. Crop each page to the way you would like for it to appear in the Kindle DX (this is good to get rid of side notes).
3. Save the pdf.
4. Now go to File–>Export–>Image–>PNG
5. Create a folder to place the exported png files
6. Now with the same pdf open, go to File—>Create PDF—>Merge Files into Single PDF
7. Click on the Add Files button, choose Add Folders, and choose the folder you created that has the png files.
8. Click the Combine Files button at the bottom right.
9. Name the new pdf and save it.
I hope this helps!