>I'm trying to figure out how, too. I'm replaying through the whole game again, not skipping the opening, opening all treasure chests, using the 0721 code for all the item shrines, and worshiping all statues and doing all events to get only positive karma. I will report back with results.
So, bad news… I just ran through the entire game again, opened all treasure chests, used the 0721 code for all shrines, worshiped for all positive karma and doing all events to receive positive karma. And nothing new. Yellow and red crystals are still a mystery.
Next step: I'm going to backtrack from the last boss in hell, all the way back to the very beginning of the game, talking to every NPC and interacting with every object along the way. Hopefully I will find some event that was missed. Will report back later.