The images are being cropped because they extend to the edge of the page. I think the easiest way to overcome this is by using an imposition. If you use an imposition. With the samples you supplied you might also prefer to have the material presented in landscape mode.
To get page labels evenly scaled, the best solution is to first create an intermediary PDF with the scaled material, and then use that to superimpose the labels.
These are the steps I suggest:
In Document Settings:
1. Set Media Box, under Page to Original Size.
2. Turn off page labels.
3. Under Impositions Take Margins From Printer.
4. Click OK button.
From menu:
5. Select Impositions->Template->Impose 1 page per sheet side. (Or press command-option-1.) [The material is now imposed onto pages, using the margins we set earlier on.]
6. If the material ends up in landscape orientation and you need portrait select Impositions->Default Orientation->Portrait.
7. Select Impositions->Replace Master with Imposition.
8. Click Proceed at the warning.
9. At this point you would turn on page labels, but it looks like a bug in PDFClerk causes those not to appear so:
9a. Save the document.
9b. Close it.
9c. Open it again.
9d. Turn on page labels in Document settings, setting font and font size, and label placement as desired.
10. Print document.
You should now have uniform page labels and no cropping of any material.