I am finishing a rebuild project where I replaced almost the whole drive train and today I was adjusting the shifting. I am almost done except that I have a clicking sound coming from my rear cassette. What I found out was that some of the teeth in the middle cogs where hitting or catching the sides of some of the chain links. Because you replaced your chain ( as I have also), I wonder if that is what your problem is too. I have not had a chance to do this yet but I think all that needs to be done is adjust the limit screws so that the rear derailer is more centered within the chain links.