Being as I am your recently proclaimed voice of anti-fluff <!-- s

--><img src="{SMILIES_PATH}/icon_e_wink.gif" alt=";)" title="Wink" /><!-- s

--> I feel compelled to point out that nothing in the above implies to me that he has been breaking into your dreams.
You had what seems to be a rather unpleasant encounter with someone who you cut all ties with. After the passage of time, something triggered you to dream about him, you let off some emotional steam, you continued to dream, you got bothered by it, you put a crystal under your pillow and the dreams stopped, the dreams came back one time when you slept with the crystal sans charge.
To me the only issue is what was the trigger to the dreams.
It
could be that this individual is someone accessing you astrally or similar and disturbing you (though I don't think he has assaulted you in any way, from your descriptions).
Or, it could be that he symbolises something to you - possibly without you being aware of what - and your subconscious is using him as an image to deal with some of those issues.
Given that your post was just a general outline of the situation I can only be very very vague here, but given that he had a clear sexual interest in you and was willing for two relationships to either end or get messed up to further that, if it was him somehow visiting you I would expect him to try to achieve those sexual goals.
In the dreams, this character seems to be setting in motion events that will have a serious negative effect on someone's life status - possibly getting you pregnant (loss of contraception), getting a woman demoted, etc. Is there some life change you are anticipating that bothers you, or that you fear? (Armchair psychology of the vaguest kind.)
It might also be worth noting that (let me see how well my memory of dream research holds up) it takes something like 2-4 weeks for regular events in the waking world to regularly filter into dreams - depending on how long it is since you last interacted with him, that could explain the delay.
Oh and one final thing - if the amethyst is giving problems, even by just having to remember to keep it charged, I'd say ptooey to that and use a chunk of black obsidian. Don't bother charging it, saying magic words, or centering. Just plonk it down under the pillow and enjoy the sensation of your mind being cut off with reinforced concrete walls.