I would like to know while practicing Kriya, will the link (thread) from Muladhar center to medulla should be a straight line or it has to pass through the Chakras. I am asking this question because if the link (thread) has to pass through the chakras then it would be in standard S shape as our physical spinal cord is in S shape. Awareness will than move from root chakra to swadisthan and then to navel and so on.
You are confusing the PHYSICAL spine (vertebrae, spinal cord, etc) with the ASTRAL (energy) spine, where the chakras are located. They are different and located in different places and dimensions!
The Astral Spine is the place through which you should be "running" prana (life-force) when you are practicing Kriya Yoga. It can be imagined as a hollow tube, about an inch and a half in diameter, running very straight up from the base of the spine (Muladhara or 1st chakra area) going through the middle (central core) of the body (which places it mostly in front of the S-curve of the physical spine).