They`ve gone yellow simply because they have done what they are supposed to do and are dying back. The rotten potato at the base of the stems is the original seed potato, and should be burned or binned.
I can`t tell you what the small holes under the skin might be without some more information, but they are probably some form of underground pest.
You shouldn`t grow potatoes on the same patch for another 4 years to avoid the risk of a build up of soil borne diseases and pests.