WCU resets whatever configuration you had in Priv when it installs, so you have to run the "Setup Privateer" program again (the one that sets the video and sound stuff). Other than that, I have no idea.
Kill lots of Retros and pirates when first starting out. At one point I was friendly with both the Kilrathi and Confed at the same time, because they both hate pirates (which I find rather odd actually).
Voyager? I guess a Drayman might look somewhat like Voyager if you squint really hard. Some jump points are just marked by buoys, no swirling sphere thingies (which is by design I think). What I found odd was the amazing invisible Jalthi. Evidently quite heavily armed for a ship that is...