Your account of the moment of origin of EMDR sent a chill through my spine. It was reminiscent of Einstein's famous ride on the commuter train -- actually more like Gautama pausing under the Banyan tree, because of the personal significance of your moment. That would make you especially vulnerable to those arrows of skepticism and it's a great relief that none of them reached your heart.
I read your response late last night and awoke with a vivid memory from my undergraduate days. One of my most influential teachers at college was Leslie White, the distinguished (and somehat eccentric) cultural anthropoligist. White took fiendish delight in debunking myths ("What fools YOU mortals be!") and saw science as the cure for the boundless distortions that are part and parcel of the uniquely human power to make and grasp symbols. Forty years after his lecture, I can still hear White's rhetorical question/mantra uttered in a tone that would do justice to Howard Stern, "Do you REALLY suppose that an ape can believe in holy water?" This was said in a way that made it clear that the ape was on the right side of the argument. For White the essence of science was doubt and he coined a verb to describe that essence: Science is NOT-knowing.
It's clear from all you have said above that you embrace fully the scientific paradigm and the fundamental skepticism at its heart. I invite your comment (even though I know I haven't really framed a question).