The pdf files had security enabled to limit assembly, page extraction, etc.. so i found a neat little program PdfCrypt.
Since i didnt know what the password was i just used it with the optional empty password and voila! Open document.
C:\>pdfcrypt.exe ch1.pdf unlocked_ch1.pdf "" 11111111
I created a batch file to process all the pdf chapters and then i was able to construct them into one single file. A little bit of work will make my life easier for weeks to come.