There are multiple levels of Colnago CLX 3.0 (105, Force, Ultegra, Ultegra Di2) and I don't understand why people are willing to name prices without knowing which level we're talking about.

For $3000, it is most likely that the OP got the 105 version. If it is parted out and sold piece by piece, I'd speculate that he could get 1200-1400 for the frame, 150 for the shifters, 150 for the crank, 100 for the wheels, maybe 200 for all other parts combined.