Distortion of exported/linked graphics

We are using InDesign CS4 for documents relating to a printed test. This test consists of a book containing over 20 different documents. There is also a scoring key and that's where we are running into problems. We exported the book to a PDF file which we are using for printing the test book. For the scoring key, we created a new InDesign document and linked the PDF of the original test. Then we added a layer and created the scoring key indicators on top of the linked book graphics. To print the scoring key, we simply hid the layer with the original test and printed only the scoring key portion. This works great with one exception...the imported graphics are not the same size as the original InDesign documents. This causes the scoring key to be wrong resulting in obvious problems when using the scoring key on the printed tests.
We have tried sizing the imported graphics up, but it doesn't seem to be a plain sizing problem; the image is actually distorted. I'm not sure whether the distortion occurs when InDesign exports the PDF or when the PDF is linked in as a graphic.
I could copy the book and associated documents and then add the scoring key layers to that but I'm hoping to avoid having all those copies which leads to confusion when updates are made. Also, the test is in two different languages with two different scoring keys so, if we went that route, I would have four copies of each of the files.
Is there a way to resolve this challenge without using multiple copies of files? Or to export and then link a PDF file that more accurately follows the original InDesign files?

I would consider taking a step backwards right here and removing all the currently placed links pdf's. The process of selecting everyone with each tool to verify position is going to be cumbersome.
Assuming you have placed the scoring key on a unique layer, delete the placed document layer. Create a new replacement. Use one of three excellent scripts for placing multiple page pdf or InDesign documents.
Test one to a few pages in the script, to verify Place to Trim, than run it on all pages. IMO a quick fix.
Do you have, are you aware of Scott Zanneli's (?) Place Multiple Page script?
Peter will have quicker access to the link I expect.

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