I went the approach to getting the raw data out of the PDF, then making use of Word or TortiseSVN, or WinMerge, etc...to take care of the comparison piece. In my instance I did the comparison in a RichTextBox in C#...coloring the differences, etc...since we wanted it all within our app.
Here is what I did...
PDF comparison as I was trying to compare mixed documents, Word and PDF.
However I would recommend PDFBox for the parsing, a bit more elegant...although iTextSharp worked out ok...