The Crystal of the Elder Things is used "to avoid paying the entire Sanity cost of a spell." You avoid paying the cost, but it still has a cost. If a character with 3 sanity wants to cast Call Ancient One, then s/he cannot pay more than 3 trophies, and it does not matter if s/he has the Crystal. The sanity's cost is at most 3, and if it's higher than 3, she can't meet the cost and therefore can't cast it
Hee hee, this is getting to be fun... it's a maddeningly poorly-defined semantic issue!
I agree that the spell still 'has a cost' even though you avoid paying it. But saying that you therefore have to have the required amount of Sanity seems to imply that there's a sort of 'check' step during spellcasting, when you look to see if you've got Sanity at least equal to the Sanity cost, and if you don't, you're not allowed to cast the spell. There's no such step - the AH rulebook doesn't have that kind of nuance. It just says:
"...To cast a spell, an investigator must pay its Sanity cost and then pass a Spell check. To pay the Sanity cost of a spell, the player simply removes a number of Sanity tokens from his total equal to the cost of the spell. Players must always pay the Sanity cost of a spell, whether or not the investigator subsequently passes the Spell check."
That paragraph doesn't bother to draw a distinction between being able to pay a San cost and the act of actually doing it. It simply tells you what you have to do, and as far as it's concerned it has therefore made it impossible to cast the spell unless you do it. The rule is simply phrased, and Crystal of the Elder Things flatly contradicts it. Whichever way you think Crystal works, it overrides the bit that says "an investigator must pay the sanity cost". With Crystal, you don't have to pay the San cost - you don't actually have to lose any Sanity, whcih is the one part that surely everyone agrees on. But once that rule from the rulebook has been repealed, there's no seperate rule which says "You cannot cast the spell unless you have the Sanity." The sanity is a cost, and a cost is a sort of check. If you're exempted from the cost, you're exempted from the check? Still with me?
Regarding CAO: your rigid order of spellcasting will probably work, but it is different from the one in the rulebook. Sanity cost comes first. Using CAO, the actual order of what happens is:
1. You discard X monster trophies and/or gate trophies.
2. You pay X Sanity (the first part of 'casting' the spell).
3. You make a Lore (-X) check. (the second part of 'casting' the spell).
4. You discard Call Ancient One.
5. If you passed the Lore check, the Ancient One immediately awakens.
6. Remove X tokens from the Ancient One's doom track.
At some point in that sequence of six events, the value 'X' has to be defined somehow. You cannot change the sequence of the effects, since they're made explicit by the card. So X needs to be defined in Step 1, when you discard trophies. That's the only bit which definitely happens first, since it's before the word 'then'. The only conceivable way to determine 'X' is for the investigator to choose how many trophies to discard. You can't define X in terms ot Sanity or Lore first, because you can't get to those steps until you've already resolved step one. This solves the Planetary Alignment problem, and any other problems to do with modifiers to the San cost or Lore check: by the time you get to those modifiers, the San cost and Lore penalty have already been defined, and those numbers can therefore be overriden and modifier just as easily as if they were printed on the card.
However, this is all based on a very literal reading of the card, and actually AH is not very clear on things like timing conflicts anyway.