How to clean an stone-stricken carbon MTB without doing damage to the carbon....?
I would clean the area with soap and water. you can cover any deep paint chips  with clear nail polish. Gaffers tape which I assume is similar to  duct tape will not provide adequate protection. It degrades when exposed to sunlight and the residue left after it is removed is tough to  remove. There are several companies making frame protection films. "Lizard Skins" is one I am familiar with. It is a thick  plastic  adhesive backed film. The film comes in precut shapes to mount in specific areas. When the film gets to the point it needs replacement it peels off. Any glue residue comes off with alcohol.