Yes, I agree that Indy knowing how to spontaneously repair ancient Atlantean machinery is a bit unbelievable (he's an archaeologist, not an engineer!). The orichalcum machine is definitely staying, but carrying around a cup of molten metal by hand simply isn't practical, so I'll have to come up with something else. The sentry statue will also be present, but not in the dungeon room. I think the lava tiles will be used as scenery rather than the actual path to the colossus island, since no human being in his right mind would walk across crusted magma. That's just suicide!
But those are all good and valid points, and have been duly noted. Thank you all very much for addressing them. Please feel free to add anything else that comes to mind!