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I figured out what my issue was.
When Calibre converts a book, it looks to split pages at 260K I think it is. It will also look to split at each chapter. Because of the format of my book, it did not recognize the chapter splits so the files were long.
My solution was to download Sigil from code.google.com and use that to split the files at the chapter level. Now everything is fast again.
I guess I could have changed the file size from the 260, as suggested, down in size but Sigil allowed me to split where I wanted to as opposed to an ambigous split.
Hopefully if anyone else is having a similar issue this will help!
Eric
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