Such an interesting case --- here are my thoughts
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I think that the killer was from Charlotte and the events were triggered by her wedding in Charlotte six weeks earlier.
1) Mary knew her killer, not as an old boyfriend, but as an unwelcome suitor from when she lived in Charlotte. He probably stalked her there, too. But, in a less threatening manner.
2) She leaves for Atlanta and, out of sight, out of mind. He probably moves on to his next obsession; or simply fantasizes about her.
3) She returns home to Charlotte for a lavish wedding on Labor Day, 1965. It's a small town, he bacame aware of it - and something just snapped.
4) From Labor Day to mid-October, he stalks and harrasses her; phone calls, flowers, probably followed her. She becomes more and more uneasy. Why she never mentions anyone's name, I don't know. It's odd she keeps it secret.
5) Around mid-October, he steals the license plate and enlists an accomplice in his plan. They probably used the accomplice's car, because he was probably stalking Mary with his own car.
6) He catches up with her at Lenox Square, probably has the accomplice make the approach. Overpowers her and drives the Comet to a dirt road and rapes and beats her. The accomplice follows in his car and let's not imagine what his role was.
7) Now, the accomplice returns the Comet because the killer wants it found. A way of telling her family, but especially her husband, that she's been taken. While I can see a sceanario, where the killer alone returns the Comet and drives out in his own car that he left parked there, I think it is unlikely.
8) Meanwhile the killer goes to Charlotte. They pay for the gas with Mary's Esso card because it's a power thing for him, plus he's not affluent.
9) They wait in Charlotte, probably someplace familiar for several hours. Poor Mary.
10) They rendevous in Raleigh with the accompice, buy some more gas, and finish it -- probably buried in woods around Raleigh.
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Takeaways -
The bank connection - it's just not as strong as the Charlotte one.
Husband Roy - probably was told by his lawyer not to cooperate with the police once they began casting suspicion on him.
The family asking to stop the inquiry - probably found out she was dead and were intimidated themselves. Not to mention painful, everytime she was in the news. (This probably applies to Roy as well)
I have strong suspicion both Roy and her parents knew who it might be and they were very intimidated. The accomplice indicates a person who had the means to take revenge even if he was jailed.
Just MOO