Another thing you will quickly run into is when doing your custom branding is the Search Centers will not show your branding. In this case, I have FAST installed on my development machine. So I went ahead and created a FAST Search center and I had the following.
First thing you may try is go to the Site Actions >> Site Settings >> Site Features and turn on Publishing just like you did for other sub sites. But doing this will not make the FAST site show your custom branding.
You can do a lot more reading on the topic on why the search text box did not appear. At the end of the day the Search Center templates were coded to work best with the minimal.master template. Recently I took the approach of trying to make a copy of minimal.master and then apply my HTML template to it. It was a lot of work and I could not get it perfect. However this brilliant guy wrote a blog about this - http://blog.drisgill.com/2010/09/converting-custom-sharepoint-2010.html
I followed his steps exactly. I made a copy of my master page, applied all the changes specified in the blog and I got the following results in five minutes. With that I now have a perfectly branded FAST search center site.
