1) and 2) I had the same issue, but decided to give up. I suspect that, perhaps, getting into the room with the barrier is only possible if you chose different solutions to certain other encounters in the game, though I'm not entirely sure.
4) I'm not entirely sure, but I think Flames of Vengeance was designed so that, if you wanted to, you could start a new character and play it. If you did that, presumably you wouldn't have the crystal skull from the Ego Draconis part of the game. I think that Broken Crystal Skull, on a non-imported character, would be a working crystal skull, to allow you to gain the ability to summon your creature. I think for import characters, it's "broken" because you already have a crystal skull. Not positive about that, but I'm thinking that's possibly true.
