We just recently updated from Cartweaver 4.0.1 to 4.0.4 and while we had done commenting somewhat, it wasn't consistent. Another idea to help those who may not have commented pages, is to use a comparison software to find differences from the source file to the site files.
I used MergeDiff (Mac) and we had a smooth update, very painless. Not only did it display code that changed, it also showed me the CSS edits and design specific updates for the main pages and provided the ability to merge them.
