First, does taking a leadership test on 3d6 mean roll three dice and take the highest two or the more straightforward sum of the three dice?
Second, how do you handle VPs for ships lost in a warp rift? Do they just count as disengaged if they "make it back"?
Re: warp rift
3d6 is the sum of the three dice. Navigating a portal that passes straight through Hell? Not an easy thing to do.
For your second question: I can't find any answer in the rules, and your idea sounds reasonable. I expect your opponent will be fine with it.