I believe the application of choice for a job of this scale would be Mif2Go from Omni Systems:
However, I'd like to point out that you have other options, perhaps the best being a conversion to XML/DITA, rather than Word. If you convert a thousand pages to Word, you will have converted a thousand pages back in time. That is, you'll be spending lots of time making your files and workflow more obsolete. Better to convert into the future, IMHO.
Although you could do this with FrameScript, as Russ points out, MIF2go would give you better quality conversion.
And you should do it by organizing the files into books, if they aren't already. You can also create meta-books or pseudo books on a directory basis to speed things up.
Just in passing, the project is unlikely to give you much in the way of documentation. The developers are developers because they want to code, not write. If they haven't done functional specs to describe what they're going to do, they're not likely to write much in the way to describe what they already did.