Is there a specific reason why you're using the "Use Paper Source by PDF..." setting?
What results you get when you deselct that preference?
"Use Paper Source by PDF Size" is used when you a have a PDF document in which a the pages vary in sizes, like for example, letter and legal mixed together accross the same document.
This setting just communicates a small set of instructions with the default printer, and have the printer to be ready to expect a mix of different page sizes at printing time.
In return the printer will know from which tray of paper to pull from the legal size or letter size according to the specified pages in that document structure.
What I think is happening is that you probably have a large document that was combined from different file sources, to include scanned documents. In which case, in the "Page Sizing & Handling" section, you can manually set a page to the "Fit" or "Shrink oversized pages" preference which should work. Then you can click on the "Properties" button and select the desired page size or customized page dimesnions profile from that list. This will enforce that every page in that document will print exactly yo the specified page dimensions and page margins settings for every page in that document.
If this doesn't work , I'd suggest you use a combination of the Accessibility Checker tool an run a full report to see what the failed tests reveal.
What I usually do next is to open the "Print Production Tool" and test a few more options with the "Flattener Preview" or just custmize a printing profile in "Preflight"--->>> "PDF Fixups"--->>>"Analyze and Fix". This sometimes work and sometimes it doesn't. You will end up testing with numerous customized profiles with no avail.
When that happens, assuming that the Accessibility already reported that you have a dmaged or improper PDF structure, it is just easier to export the whole file to an image, and open it directly in Acrobat to let the PDF Optimizer and the Scan & OCR perform its checks and convert the file back to correct PDF structure out of that image file.
Now, this could be a very lengthy process, in which case, a large file such as the ones that you're describing may even crash the Acrobat program.
I've also read in the forums before that it is best to split the original file in smaller chunks (or smaller groups of pages to be prcessed at one time).
That is why I suggest in my last recommendation to save as or export to an image since they will be saved as separate image files to a folder that you manually choose; then merged them back together with the Combinne Files Tool.
I know this sounds like a lot, but if you can share an example of one of these type of large files I can recreate the scneario on my end and see what's wrong before you do any of these recommendations.
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