I did a quick online search, but, unfortunately, I couldn't find documentation of Simplify's file format. It should be out there somewhere in the Simplify source code or in an earlier release of Z3.
At the time Daikon's interface to theorem-proving was written, Simplify was state-of-the-art or nearly so. Today, other tools such as Z3 are much better (faster and more capable). The Daikon manual mentions this:
http://plse.cs.washington.edu/daikon/download/doc/daikon.html#Installing-Simplify . So, if you cannot figure out the Simplify file format, or if Simplify is too fiddly, you could consider interfacing Daikon to a different theorem prover. That is not a trivial task, but it isn't conceptually difficult since much of the work is mechanical translation from one file format to another.