The FlexWiki binaries are available by downloading continuous release packages from the project builds here
But which build do I want?
You need to decide between the full package and the update package. The difference is that the full package includes a few extra files to provide a default Wiki installation (see TheDifferenceBetweenTheFullAndUpdateDistribution for details). Whether you choose v1.8 or v2.0 you always want the latest build version. FlexWiki v1.8 uses ASPNET v1.1 while v2.0 uses ASP.NET v2.0
If you unzip the full package into an existing site, you will step on some of your configuration files. So:
if you're going to create a new site, use the full package
if you're going to update an existing site, use the update package