I ended up spending about a day manually going through and removing the duplicates and integrating the different formats into a single entry. This taught me a few lessons.
The idea of re-adding the existing library with the remove duplicates is a neat. I obviously have to do more reading on what Calibre is capable of!
Thanks to dwanthny and Marvin_2...and to the considerations raised by Pinecone and theducks! You guys are fantastic!