I have this same problem. It is obviously excel. Acrobat gives the error “Number out of Range” when you try to Save as… It actually only happens with Excel-generated PDFs in my case when there is a text box over the chart (i.e., identifying a line). If you use a legend, this problem dose not occur. Unfortunately, the legend in Excel is very limited. (The whole office for mac version is a joke actually. This isn't even a problem in the Windows version. Why should consumers suffer due to a war betwen monopolists?)
The fix is to open the PDF in Illustrator and delete the very last layer—why, as you'll see, is just out of the bounding box. It is ridiculous that Excel doesn't make valid PDFs.
One other thing: copying and pasting does not work, and I have a hard time believing you can “tweak just about everything”. I changed every setting possible in import settings and nothing helped: because it is a bad PDF, not because of ID.