The headers at the top of each page of the MPEP PDF give the section number. As far as I can tell, it's the last section number on that page. For example, p. 2100-141 (Nov. 2015) ends with half a sentence of 2142, so the header reads "2142." However, the vast majority of text on that page is 2141.03. Would it be possible to clarify which text is part of which section in some way? At present, I regularly wind up reading backwards to confirm which section I'm in before citing it.
One possibility might be to include the section number in the Roman-numeral headers. For example, on p. 2100-141,
III. ASCERTAINING LEVEL OF ORDINARY SKILL IS NECESSARY TO MAINTAIN OBJECTIVITY.
could be changed to
2141.03, III. ASCERTAINING LEVEL OF ORDINARY SKILL IS NECESSARY TO MAINTAIN OBJECTIVITY.
I understand you are likely limited to what your software can do. I also understand this is only an issue for PDF, not online. However, I frequently work offline, so use the PDF heavily. Thanks for considering this request!