First off, You can always edit your posts instead of adding new ones here.
About the link, I don't know you have to decide! Here in this post you linked to domain.com and on the site it is domain.com/index.php
Here's a protip for you: To search engines, All the following forms of links are different from another...
http://www.domain.com
domain.com
http://www.domain.com/
domain.com/
http://www.domain.com/index.php
domain.com/index.php
All of these links are different from another, You have to focus on one of them.
1. Make 301 redirects.
2. Use canonical links
3. Set preferred domain from GWMT
About the nofollow tags, I usually don't add nofollow links in posts, Because I must be mentioning them because they worth something and deserves a link :)
You don't have to be all paranoid about the nofollow tags and PR flowing to them, But at least work on the link in your home page.