By your post I'm assuming your running 2 instances of WoW on your Server PC and it's not broadcasting the keystroke to your second instance of WoW. If this is the case, Synergy will not broadcast to the other instance of Wow on the same machine. You'll need Keyclone or the like to broadcast the keystrokes.

As far as sending different keystrokes, I don't think it's possible because of the basic coding language used in identifying keys strokes. Why not just bind your "Z" key for whatever action you need on your server, then bind the same "Z" key to whatever F6 would have been used for on the client?