I tried using calibre for my kobo but it just wouldn't allow me to view the content on my ereader. So for the last coupld hours I'be been playing with font size and page size on word and then converting it to PDF. But thanks to that no more pan or crop and the pages fit the screen exactely how I want it to.
They may seem like ridiculous dimensions but here is what I used for my kobo all the numbers are in inchs.
Margins: Top:0.07 Bottom:8.4 Right:1.32 Left:1.32
After I type in the dimensions on word I go to print (I have PDFcreator) click on the PDF printer and change the page dimension to the right Width and Height and press print. Voila PDF that fits on the Kobo. You can read any font size that's larger then 20 (which is small).
Don't know if this will help or not but good luck with your PDFs.