Punctuation outside of quote marks

Is the punctuation in the following example correct? I went by the assumption that terminolgy and nicknames require that the punctuation goes OUTSIDE since they are not acutally quoted material or dialogue. Please give me your input and where you found the information to make the ruling. Thanks!

Walkerton churckfolk proudly started calling their minister “Dr. Smith”, but the new title didn’t impress the humble man. According to protocol, people were supposed to address him as “Dr. Smith”, but he never pressed the issue. He was satisfied with “Reverend Smith”, “Mr. Smith”, or even “John”, which is what close friends called him. To his wife, Mary, however, he still answered to plain old "J. D."

Along the same lines, please review this index listing to comment on the punctuation:

Johnson, William C. “Chet”, Jr.

Thanks for your help!