Reload a save from before the cutscene and go back for Zagan at a higher level; he is quit challenging in DKS. See: Zagan tips
BTW, did you find the malachite veins in the cave, off to the left just before triggering the cutscene?
There are 3 teleporters in Barnabus' cave, one on the ground and two on ledges mid-level and high up. Two of these teleporters lead to smaller caves with generators that need to be disabled, though you should go through all three before fighting Barnabus.
There is a large door in the harbour building leading inside, on the same side as the elevator platform (closest to the fish merchant).
Stone's fortress is the easiest one (teleporter on the north east end of the island across from the dragon cliff castle), followed by Raze (mountain across from the harbour), Broken Valley, Keara and then Kali (Rivertown Gorge). You can do the human sections first, and leave the dragon combat and/or headquarters until later, if you have trouble with them.
There is no way to lower the anti-dragon shields around the harbour and High Hall. You also can not get into the tower there.