Here are a few random thoughts that may help. About the two texts you link to: the first one is clearly a Theravadin practitioner, and the second one is Tibetan. Vipassana is a Theravadin technique, and the fact that the author refers to enlightened people as Arhats also indicates this. The Arhat is the highest level of realization in the Theravadin tradition, and this tradition makes no use of the Chakras. Also the meditation you described for yourself in this essay makes no reference to the chakras. I think what you have done is opened yourself up to whatever energies are available to you, and they are going every which way because you don't have any awareness of which Chakras they are entering.

I did have one bad response similar to what you experienced when I started having heart irregularities. A meditation I had done for years that involved introspecting my bodily sensations triggered an Afib when I put my awareness in my heart. My acupuncturist, who also studied with Tenzin Wangyal, suggested that I put my awareness in my navel chakra instead of my heart chakra. This drew the energy out my heart area, and defused the Afibs. The second article linked to your page describes a problem like mine, that was treated in much the same way.

I would suggest reading that article in greater detail and seeing if any of it helps you make sense of your experience. But more importantly, I think you should get some direct personalized advice from an experienced meditator in a Tibetan tradition. Your devotion to meditation has brought up some powerful stuff that is way outside my experience, and I don't think I'm competent to deal with it. You've called up some really powerful energy, not available to most of us, which you need to learn to control. Tibetans sometimes use the phrase "Wind horse" to describe this. You've got to learn how to ride that wind horse.