No matter what I do, I can't get my character to put the two swords in the stele to get the third sword. He swings, he cuts, he does everything but put the d...swords in the heads of those skeletons. Any suggestions?

Don't hold the sword in your action hand, use it as if you wanted to drop it. But instead release it on the stele. Then u put insert the sword.
Same thing as putting the crystals on their pedestals in the end.