The biggest pain I find with self publishing is that you don't get a pro to hold your hand and correct your punctuation, discover spelling errors and other boobs. I've paid for a freelance editor and found it didn't work - too many errors just weren't picked up. Now I have a friend who proofreads (thanks Julie!) and I've developed an editing system.
First I write my MS in Word. I don't use headers, footers or page numbers. Just plain old text.
When I'm done, I run a spell and grammar check through it.
I go through it again, looking at the dialogue for punctuation mistakes. It's very easy to see a full stop where a comma should be and visa versa.
Then I run thought it again and put in a global change that replaces every full stop and two spaces with a full stop and one space. This is one of my "best" errors.
I highlight the entire text and click on Format, Auto Format. I fix any visible errors.
This is the end of the first edit. Now I convert it to an epub (thanks Calibre!) and I read it on my iPad, highlighting any errors or changes that have to be made.
I wait two days, then do it all over again.
Now Julie gets to have a go. She picks up the rest of the problems, and sends it back to me.
I accept or reject her suggestions, and put together a table of contents, front matter and other sexy stuff. I convert it, and read it again.
Then I upload to Smashwords.
I know my books will have the odd mistake. Hey, I find them in books put out by Penguin, Harper Collins, Norton and other fantastic publishing houses! I don't think a tiny errors here or there is a disaster but it is better to avoid them.
Blackmail Bride had the attention of a paid editor, but Julie and I found several mistakes. Do read it! And if you see a mistake, email me?