Several have had the newer replacement shaft go back to the same problem. Do a search for intermediate shaft. Lubing it with a thick grease is about the only way to fix it. There is a tech article on doing this.
I just had mine lubricated with silicone grease last month. It took the clunking away for now. In my mechanic'* experience even replacing it will eventually produce the same clunking so I'd try lubing first and seeing how long that lasts before you spend all the time and money to replace it. My car only has 47000 miles on it.