Don't know waht script you used, but I recommend this one: InDesignSecrets » Blog Archive » Zanelli Releases MultiPageImporter for Importing both PDF and INDD Files
It allows you to set the scaling when you run it, and it will be one heck of a lot faster to just run the script again on a new file than to go back and manually scale 1299 PDF pages. The other option might be to find a script that can find the already plced pages and scale them, but I don't know of one that's already availble. You could ask over in InDesign Scripting
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You can do this with layout adjustment. Switch it off, set the margins
of all pages to be flush with the pdfs. Then switch it on. Check "allow
graphics to resize". Now set the margins to whatever size you want your
pdfs to be and they will resize.
It will still take a while for InDesign to do this to 1000+ pages, but
at least you can sit back and do nothing. But test the procedure on a
dozen pages or so first to make sure you've got it right. Also, make
sure that in the margins and columns dialog, switch preview off before
you make any changes to the margins, otherwise you'll have to wait × 4
for each change!
THANKS SO MUCH !!!
THANKS SO MUCH, ARIEL !
What do you think is missing? The nin-point proxy is repalced by the dropdown, and there's now a rotation field added....
"Position on page aligned from" is missing
Click the dropdown. You'll see nine choices that correspond to the nine points on the proxy in the other dialog and three more relative to spine.