When you "print" from the application, instead of actually printing, select "Save as PDF..." from the "PDF" menu in the lower left-hand corner of the "Print" dialog.
This should cause the entire page, no matter how large, to be printed as a single sheet PDF (36" x 48", or whatever) that is sized exactly as the document is set up.
Edit: This assumes that the original document is printed from a Mac, and that the software used to create the diagrams runs on Mac OS X.
If you don't have access to the original program to do a "correct" PDF print of the document, and all you have access to is the 8.5" x 11" PDF documents, then this method won't work.