Hey forsaken, My answer is no, a clone cannot have chakras because your metaphysical body is not part of your human body so the connection is lost. A clone is just a physical body in this 3 dimensional realm. It simply exists in the 3 dimensional realm. Father Satan created souls for all gentiles, he didn't create souls for clones. That why its so imperative to keep our bloodlines pure. Father Satan knew about the technology of clones hundreds of thousands of years ago but he didn't teach it to us because he knew it would never be able to advance to the stage of gnosis. The metaphysical body permeates our physical body, it resides within our physical body but it is not part of it. Our subconscious mind is part of our metaphysical body it forms a bridge to it, that's the reason we are trying to fuse our conscious and subconscious minds together so that they become unified. The Ida and Pingala energies from the conscious and subconscious minds attract the kundalini up our spinal columns fusing our metaphysical body to our physical bodies. This is the process of achieving the Magnum Opus and Gnosis. A clone is missing a metaphysical body so the process can never happen to a clone.
Hail Satan!