Does this carbon fiber need a clear coat?

Yes. Bare carbon fiber is susceptible to UV damage and will yellow over time without protection. A quality automotive clear coat seals the weave and preserves the color and finish for years. Apply the same way you would protect any exposed carbon component on your truck.

How do I protect the edges where the fenders meet the door jamb?

Sand and seal the panel edges with epoxy or carbon fiber-specific edge sealant before final installation. This prevents moisture from creeping into the weave at the contact point. Once sealed and painted, the edges will resist water and UV just like the main panel surface.

Will carbon fiber fenders flex or rattle when I hit bumps?

Carbon fiber is stiff for its weight, but over-fenders mounted over OEM panels will track the underlying structure. Make sure all fastener points are tight and torqued evenly to eliminate vibration. Refer to your vehicle's service manual for fastener torque values to prevent loosening over time.