The guide is telling me to collect a yellow crystal and mirrors from the collector... theres nothing in the tray. Wtf?

Are you sure that it is not set up in the dungeon somewhere (i.e., did you reset the lever?)

You missed a step. You're going to have to go back and retrace your steps pretty much. Match your quest log up to the quest guide.

either that or you haven't pulled the lever to reset it. also, good luck with the quest, it is a little bugger to complete.

You should try to use the lever to reset the dungeon. If you still don't find the yellow crystal, it is really strange. But you should find it in the tray if you just pull the lever.

Good luck with the quest, it is a hard one.