After considering the great problem of assigning Chakras to the Serpentine Lords, I could finally conclude that:
Ketu ruled Chakras:
The Odd numbered chakras of 1. ROOT, 3. NAVEL, 5. THROAT and 7. CROWN are ruled by Ketu. They signify individuality, intution, self, Ego, intution, spirituality
Rahu ruled Chakras
The Even numbered Chakras are ruled by Rahu: 2. Sacral, 4. Heart, and 6. BROW. They signify Harmonisation, blending, flow, perceptions, thought, materiality.