For those on the receiving end, here are some tools and suggestions to give you a boost. First and foremost, keep a good backup of the source code, and a log of each of your revisions. The best way to do this is to place the whole project into source code control, and religiously check in any edits with appropriate comments. Next, you need to be comfortable with your text editor. It needs to have a rather flexible search and replace, and should be very good at comparing files or folders of files.
Nothing is as hard to undo as a poorly chosen global replace.
The biggest mistake you can make is to jump into the source code and start hacking away. If you aren't familiar with the structure of the project, you should start by making only minor fixes and improvements until you get your bearings. When you have a big list of changes to make, you should break them down into moderate chunks. Major changes to the project structure or functionality should be planned so that they mesh well with the established framework. Finally, it's important that you try to avoid optimizations the core engine of the application unless you are intimately familiar with it.