Dr. Zaus
Lifer
Word was only software used, other than InDesign to handle the formatting for print and epub.
I created a general outline and notes on each of the characters, and put the book together at night and on the weekends. It took roughly 3 years to get it close to the current iteration. I hired an editor a little over a year ago and spent most of 2011 integrating some of his suggestions and changes into the work.
Wow.
About the cover: this picture made me think of.