I don't know of a way to prevent a double inclusion, other than getting an error message that is. Are you seeing includes placed throughout the page, which is making them difficult to spot?
Just as an aside, are you working with a copy of the code and the database on a development server? From my experience, the first thing to do is separate yourself from the live site ASAP. While a hassle initially, it'll give you the freedom to make changes without messing up the live site. It's easy to make that one tiny change in an include and BAM! the whole site goes down.
I've worked through a few projects like you've described and used the following strategies:
Complete rewrite - perfect when there's time/money, but usually I get the call when something has gone wrong and results are needed ASAP.
Smaller projects - I open up everything in the IDE and just start searching all the project files for the functions/sub, in order to build a knowledge of the include logic. Pretty much each time, everything is spread out everywhere, so I start rebuilding the includes organized by business logic. I've also run across inline code (raw code, not subs or functions) thrown into an include, so I'll usually just pull the code back into the page for refactoring later.
Larger projects - I'll use some code I have laying around to parse the includes for lines with sub/function headers and dump those to a text file to build up a list of what routines are where and refer to that. This comes in handy when you've got a ton of includes on each page and can't get your head around the codebase.