So today I played around with the Foundry for the first time [awesome tool btw, it's very easy to use!], when I came up with a few questions:

1.) I was trying to make a deep space encounter where one of my allies is a Galaxy Class ship. How can I do that?

2.) Is it possible to give yourself a costume just like in "The hour of the comet", where you become a Klingon D7?

Have the same question, ¿there is any way to make the NPCs moves?

1) Yes! You can create a custom ship in the costume editor, and then drop it anywhere in your custom map.

2) Unfortunately, no.

There is an option to turn on the NPC wandering, but it may be bugged at the moment. No matter what value I set the wonder to, I can't get them to wander.

I just tried it with the costuming editor; it works with the contact vessels, but they just sit still and don't fight with me. If I try to assign a costume one of the Encounter NPC group vessels, they keep their appearance and ignore the costuming.

Have you tried setting their behavior to "Ambient with Combat"?

I dunno if this is a solution, or a bug - but I was having a problem with NPCs not wandering properly. And then I turned off the wander setting... and now they wander. Might be something you can play around with - I haven't yet had the time to look into this further.