As Aaorn Digulla noted, a wiki is a great idea. You have to realize that the only way you are really going to achieve what you want is to rethink your entire document strategy.
No software is going to fix the issue of incompatible file formats and not being able to compare different versions. The tools you are using now are the wrong tools for the job. It's going to be tough, uncomfortable, and possibly expensive to change your toolset and your way of thinking, but that's the cost of being able to achieve what you want, which will end up paying for itself 10 fold.
Just think back to the difficulties you had initially with schema docs, UML diagrams, and even something as simple as planning out a Word document. Those worked up until this point and they got you this far, but the only real way forward is to move on to tools that were designed for what you need now.
Note: the ultimate solution might not be a wiki, but it's definitely not what you are using now, either. You need to explore a bit and try a few things out.