@CWatkinsNash,
If you're interested in my two cents, I just went through the process.
The best thing, in my opinion, is to start with a clean ePUB. You can get that from Sigil (free!) and Sigil is perfect for fine-tuning. You can also load the ePUB in half a dozen computer ePUB readers and view how it will look (Nook app, Kobo app, Aldiko, Moon+, etc.). You can then load that ePUB directly for sale on
B&N and
GoodReads.
Next step is converting ePUB to mobi. I tried the Amazon conversion, the Calibre conversion, and a couple of online tools, and the Calibre conversion was by far the best but there were a couple things (like the TOC location) I didn't like that I couldn't figure out how to fix by hand. Oh, well, the reader most likely won't notice. Load that mobi onto
Amazon for sale.
Next is the
Smashwords (Kobo, Sony, Diesel, Apple) word doc and yes that is a nightmare (for me). I went ahead and gave 52 Novels (Konrath's formatter) $75 to just format the dang thing themselves. And even
they can't promise "perfect" 1:1 such that my starting ePUB matches the ePUB that Smashwords produces. And they do this for a living. Anyway, it takes 52 novels about 2 weeks to do their thing.
Two weeks is significantly shorter (in my mind) than the Amazon 90 days. Plus, GoodReads and B&N are immediately available.