I don't know about chakras, but 'Chi' followed imaginary conduits through the connective tissue that... turned out actually there are conduits through connective tissue for lymph to move. They're just really really tricky to image so we didn't know about them until about ten years ago.

I took a Yoga class years ago (my tight wrists made it very unpleasant) and on the last day of class the instructor pulled out some obscure stuff and had us do some energy work, which I was sure was going to be complete bollocks. And about five minutes before the end of the class I experienced feelings that were identical to Flow state (that slightly buzzy feeling when you're in the grove and just crushing a task.) I recall thinking, "Oh this is potentially addictive. I'm glad this is the last class."

I'm betting that 10-20% of the mysticism stuff eventually turns out to be true and the rest is speculation built on top of correlation with those objectively true bits. Science eventually gets around to studying coincidences. Medicine tends to be more arrogant and dismissive of anything they can't measure, for far longer than is strictly healthy.

Sort of, but it generally goes more like: base/perineum, genitals, navel, heart, throat, forehead, and then one at the top of the head or just above. The Sefer Yetzirah, however, references specifically "Head, Belly, and Chest" as the three loci of the human body. (§ 3.4-5)

Gurdjieff was literally, physically correct: we are three-brained beings.