A quick glance at your code, already shows a first error:
the following line takes effect on the next page:
>      document.setPageSize(reader.getPageSizeWithRotation(j));
This will be ignored when the current page is empty:
>      document.newPage();
So you can't expect the first page to be OK.

Furthermore, I don't understand why you want to use
PdfWriter and PdfImportedPage in this case.
Depending on your exact requirements, it may be
more interesting to use PdfCopy and/or PdfStamper.
br,
Bruno

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