I will be revising the website of Homebrewzone.com. Though the website is to out of control to completely fix, and with multiple other Homebrewing sites that are designed much better and in better repute (Craftbeer), I will still analyze the site's faults for the project.
The first problem is of course the welcoming page....it should be a homepage. It is cluttered and disjointed. It does have links to other parts of the site, on the left hand side, but these are right under the label "Ads by Google", which always makes me wary. The website name in the upper left hand corner could also be bigger in order to catch my attention, and an overall template that represents professionalism is missing from the site. Some of the smaller "How to Use" sections could be put into a section under a heading on the homepage in order to make the site more organized.
Another part of the page that I want to break down is the Glossary of Terms. This portion of the site seems well organized at first, with bold words and regular definitions, all in alignment, but it is missing ease. In order to get to a word I want to find out, I have to scroll all the way down the page. It would be much more useful to have an alphabetical quick link at the top to get to the letter section I want. Also, It would be helpful to include pictures with some of these definitions. Some of the tools described are not used outside of homebrewing and someone who is just starting may not be able to picture the tool just from the definition.
I also will be looking at the Brew your Own Beer section. I believe it would be much smarter to name this section something like "Getting Started" or "Brewing for Beginners", because that is exactly what it is for. It is also in the format of one long list. It would be much better for each step to be hyperlinked to a different page so the reader can grab and go. That way all the steps are listed right in front, above the fold, and ready to be clicked on when the time comes. The long list just makes it difficult to follow and easy to lose your place in, which is not good when brewing time comes around and you are knee high in wort and needing to add specific ingredients at specific times.

Cory,
I think this is a great site for revision for this project. There is a lot you can do. I agree with the points you already raised. Another you might consider is whether the 3-column format works for this site, or if a 2-column format might work better. But there is a lot of fodder for revision here. I think it will work well for the final project.