I am familiar with some of the basics of fparsec but it seems to be geared towards text files or streams.
Are there any other F# library's that can efficiently parse binary files? Or can fparsec be easily modified to work efficiently with binary streams?
You may be interested in pickler combinators. These are a bit like parser combinators, but are more focused at simpler binary formats (picklers allow you to produce binary data and unpicklers parse them). There is a quite readable article about the idea (PDF) by Andrew Kennedy (the author of units of measure).
I don't have much experience with these myself, but I just realized it may be relevant for you. The idea is used in the F# compiler for generating some binary resources (like quotations stored in resources). Although, I'm not sure if the F# compiler implementation is any good (it is one of those things from early days of the F# compiler).