Can new ridge caps be installed over the existing caps?
No. You should remove all existing ridge caps, then apply a water proof strip of felt, metal, fastener-sealing eave protection to ensure that the ridges or hips are water tight. Finally, install the new ridge caps.
What is the appropriate fastener length to use for over roofing applications?
Assuming local Building Official approval for this type of installation is obtained, you should use the length of nail recommended for that specific material. Add the thickness of the existing roof and this gives you the nail length required for the fastener to penetrate ¾" or more into the sheathing. Refer to the CSSB's New Roof Construction Manual.