Debugging Sitecore 404

Recently, I was baffled with Sitecore throwing 404 error page. This makes things even more so confusing with the following status/checklist

1. Site used to run
2. There is no code changes. The only change was domain name
3. IIS Binding has been configured with the new domain
4. Site is up and domain has been pointed to the correct webroot. I tested this by dumping test.txt on webroot and try to access it by /test.txt. I can get the text file.
5. Changes also have been made on Site definition to relect the new change in domain name
6. Sitecore backend can be accessed
7. I have checked the item exist in backend

Finally i figured out the problem when i inspected the url for the 404. It looks something like below

http://domain.com/Standard-Items/Error-Pages/Page-Not-Found.aspx?item=%2f&user=sitecore%5cAnonymous&site=scheduler

As you can see, the query string "site" is scheduler. That's not right, it should be "website". So I look at site definition again for error