I knew someone who had a very bad low end but it was because his pistion rings were gone. If you say that the engine was just put in, then I doubt it. Was the timing done right? When my ST205 was put in, they did the timing wrong, and it was very laggy but it is hard to say as I have a different turbo too.
The CT20B shouldn't be a problem, as they are quite strong, just don't overboost it as if it blows, the you cannot repair it. Are you sure the Turbo was in good nice when you got it?
Anyways, I don't think it is the actual turbo. Sounds strange man.
Was the manifold and and turbo all bolted properly? No leaks?