I have been running over ideas in my head, trying to sort out the best ones before I make my first mission. That said, is it possible to use the borg or aegis parts on npc ships (given they can be used on said ship)? Just curious so I can check or cross off an idea I had.

Not as far as I am aware. It's based on equipment and not on actual ship costume. It could be implemented later though, who knows.