I was facing the same problem. One file containing the odd, one file containing the even pages of a scanned book. I simply used the built in Windows 7/8/8.1 batch rename capability.
1) Split the pages of each pdf back into seperate files for each page such that one folder contains all odd pages as seperated files and a different folder contains all even pages.
2) Bulk/Batch/Mass rename the files of both folders in the same way. Simply select all files in each folder and rename the first one as a and hit enter. In doing so, the files in each of the two folders will be numbered as a(1),a(2),a(3)...
3) In the folder with the odd pages, copy all files and paste them directly into the same folder. In doing so, it creates copies of the files with the odd pages that will look like a(1) - Copy
4) Move these copied files to the folder containing the even files. This sorts them in front of the even page files (as long as the files are sorted by their names).
5) Merge the the files back into one file by simply following the new naming scheme.
In order to merge and split the pdf files I used pdfIll's Pdf Tools which is available for free.