your story looks pretty cool. i was thinking about the problems with taking over larger capships. i guess if you've already rewritten your stuff then this won't matter, but its conceivable that the GTVA might have something like the 'prefix codes' that were used in star trek 2 (sorry for the blatant ripoff). i mean, if you think about it, there has to be some way to remote control at least part of those big ships - having 10,000 people always around to do every job is unfeasbile. maybe the NTF nabbed the code(s) for some GTVA ships and remote controlled them. you could even go so far as to say that they could just open all the airlocks remotely, waste everyone, and then claim the ship(s) for themselves. that's my 2 cents worth. good luck with your story! it sounds good.
i know how beams work.