I've been waiting all my life for someone, someone who nows how to make good chocolate to make caffein-free chocolate: http://daisybrain.wordpress.com/2009/09/25/free-ideas/
I think it would have a huge market for those who love the taste but can't do the caffein or for parents who want caffein-free chocolate treats for their kids. Am I crazy? What's the problem? It's my understanding that it would be as easy as decaffeinating coffee.
The webpage mentioned on your blog is correct in some ways (chocolate's main stimulant is theobromine, not caffeine) but wrong in many other ways (chocolate does contain minimal amounts of caffeine, mateine in caffeine is NOT a stereoisomer of caffeine as that is chemically impossible, like saying the mirror image of a chair is totally different from the original chair) so take what it says with a grain of salt.
So the main stimulant in chocolate is theobromine, but not everyone responds to it as much as caffeine. In one study only 2 out of 20 people could feel any difference from fake chocolate bars made with and without theobromine. It's more likely that the stimulant effect of most chocolate comes from the sugar in chocolate bars (~30% in good dark chocolate and up to 50%or more in milk chocolate) and the other minor psychoactive compounds in chocolate like phenylethylamine (like the street drug MDMA), serotonin, cannabinoids, dopamine precursors, tryptamine, beta-carboline alkaloids, and more. So taking the caffeine and theobromine out of chocolate may not really reduce it's stimulating effects, though it may help people who are alergic to these similar alkaloids.
Given that, it may be possible to decaffeinate and detheobrominate cacao using the standard water or dimethylchlorate techniques though I wonder if the fact that more of the flavor compounds in cacao are water soluble vs. the more oil soluble flavors of coffee, if these techniques based on the solvent's polarity would take out more of the cacao's flavor than just the caffeine & theobromine. It would take some serious experimenting!
Nat Bletter, PhD