As Kundalini energy moves through the body various issues, even pain, can arise in chakra areas. Usually a person who has activated kundalini has not prepared themselves in the ways recommended in classical kundalini yoga. Some systems say 12 years of preparation is required before the energy is awakened if all is to move smoothly, and this is done through physical cleansing practices, strict diet requirements, gradually adding more advanced breathing practices, sitting in specific yogic styles, and releasing various egoic tendencies through obedience to the teacher and system. It is clear that 99% of those who activate this energy have not done these kinds of preparations and are not interested in doing them. In some cases, yogic masters say that a person who has activated energy spontaneously must have done lifetimes of work previously for this to happen. But our present bodies have not been present during all those lives, so they need adjustments and releases.
My perspective is that many factors come into play to cause a person to be available to this opening (which I have enumerated on my website and in my books) but most often there is a long and gradual process as the subtle body energies, physical body, and psyche adapt to this new energy flow. One must be patient and take time to address old psychological issues and to adjust their life to the new patterns the kundalini energy is calling for. So when there is pain in the body that doctors find no reason for or heat arising, or strange blockages where energy seems to be stuck this is because some clearing is needed since it was not done before the awakening. Some spiritual seekers believe that an awakening will erase all past psychological issues, but if this should happen it is only temporary. Some old beliefs, preferences and habits will fall away or transform, but deeper issues will then come to the surface, and the energy must return to clear the blocks that were created by these experiences. For an awakening to become stable and comfortable it appears that we have to see through all our old patterns, holdings and attachments, recognizing they are not definitions of who we are. Until this happens we are likely to feel divided, or caught in "I got it. I lost it" syndrome, seeming to fall in and out of positive awakened states.
One commenter asked about pain in the neck and shoulders that seems to have no medical source. This is the area of vishuddha, the throat chakra. There are several possibilities for this kind of pain. Energy is often blocked here because most of us spend a lot of time holding back our self-expression or our emotions. It's as if everything unsaid is locked into our subtle energy field. Sometimes spiritual seekers believe they should never feel anger, and so when something outrageous happens to them they swallow their feelings in order to be "spiritual" and forgiving. I met one person who seemed to have tourette's symptoms as his face jerked spontaneously, but once he released anger these problems went away. One does not need to act out the anger, but simply find a safe way to move it out of the body through expression by yelling (at no one) or writing and just fully acknowledging it.
Another reason for pain may be an old injury that has been locked in the system and needs to be released. Kundalini seems to be trying to remove anything tight or damaged in the body. Some call these blocks. Wherever your energy seems stuck and keeps returning to with jerks or discomfort over and over is generally seen as a block, caused by physical or emotional holding from issues in this life or possibly a previous life. Sometimes it is even an issue related to your birthing experience, or your mothers experience when you were in the womb. Also a stiff neck may be caused by the way it has been held for years, and gentle body work can help to open it. Cranial-sacral work or acupressure might be useful.
In yoga there are 3 major "granthis" or "knots" in the body which must be released in this process. These are believed to be points where the power of ignorance and attachment is particularly strong. One is in the solar plexis area, where we are attached to pleasure, material things, and having things go our own way; the second is in the heart area where we are attached to our emotions, certain people, our personal visions and passions; the third is in the the third eye area where a person may open and then become attached to psychic powers and attribute them to their personal identity.
So as energy moves through to change consciousness and make your energy field as open as possible, these are a few of the clearing challenges that may arise. They can be addressed through therapy (if it is rooted in a past traumatic experience), using sounds such as the Bij mantras to open chakras, yoga postures that are for stretching and relaxing that area, meeting the pain directly with presence and love, guided imagery, acceptance and surrender and in other ways that you might intuitively discover. Taking good basic care of the body is important in this process and releasing personal demands that life be just the way you want it -- learning to live in the flow of the river -- as the Taoists say-- is helpful. This is why quieting the mind or at the least not being driven by thoughts, can be helpful. Our thoughts are often focused divisively, telling us what is wrong and worrying about it, blaming us and others for it. Bring awareness down into the heart or the belly and see if you can be present more fully where you are at any moment. This calming will support the opening of intuition which may be able to suggest some new directions to resolve those challenges in your process.