Arbiter of Divinity Issue

While progressing through the end game tutorial fights a friend and I did it together. I didn't run the maps for the key pieces themselves, however after the fight it gave me one of each. I attempted to do it solo but failed, now I cannot do anything and am hard stuck at the Arbiter of Divinity portion. It didn't give me the Atlas Passive Points but did let me allocate nodes past where it was locked previously. I have since farmed up a Origin Spark and Origin Core - but it will not let me put them into the Engine. Please help!