Create a Content Audit Document
When I do this I create a Content Audit Document, not dissimilar to the one shown in this article. I've played around with using databases, but usually just stick to Excel.
Each page is uniquely identified, and had several attributes (these are the columns) like URL, Title, Description, etc.
Define Some Key Attributes
The attributes are the key, and should be representative of the concepts you are trying to document. For example, I once audited a Tech Support site and one of my columns was called "Has browser pic?", and each page had either 'Y' or 'N'. At the end, I could easily see where all the screenshots of browser windows were, and when I had to delegate the task of updating them all, I sorted by that column and easily created a list.
You'll have to be creative and come up with column headings that are meaningful and actionable e.g. "Color Deviation" (Y/N)
Put On Some Music and Audit!
Then you have to visit each page and mark whether the page has any of the attributes you defined.
You'll almost certainly make up more attributes as you go along and have to go back in fill in values for previous pages.
You may find that you can save time by working at at different level e.g. subdirectory level as opposed to page level.