So I was able to load a book from Calibre onto my KT with no lag at the processing stage! I went back to using Calibre 0.8.5 and ejected my KT from the list of devices in Finder only (rather then with the eject device feature in Calibre). I also gave a little bit of time (around a minute) between loading the book and ejecting and ejecting and actually disconnecting the reader. I'm so happy it's all working again! Thanks to everyone who helped, you guys are great.
Now back to the reading!