I ended up using Gregory S. Chudov's C# implementation of FLAKE encoder. You can find more information at http://www.hydrogenaudio.org/forums/index.php?showtopic=74242
There is another project on BitBucket that uses CUETools FLAKE in its Google Speech Api wrapper. It is a good starting point for implementing speech to text using Google speech api. You can find it at https://bitbucket.org/josephcooney/cloudspeech
I was able to convert wav to flac without much difficulty using the FLAKE encoder. Hope this helps you.