I bought a CD3 new and had it for several months before having the opportunity to get it upgraded to the MkII. So I was very familiar with the overall sound in my system. The MkII is a definite improvement assuming your system can reveal it.
I found a better clarity in the highs, with even more resolving of inner detail. Very delicate and quiet sounds (such as light drum stick taps on the symbols) seem to focus better within the image. The harmonics of sustained high piano notes seem to last longer and float better. If you appreciate and listen for this detail, you will be quite satisfied.
I have found that I can listen to the CD3 for hours at a time absolutely without fatigue, and the MkII makes it even better.
Is it worth $1K? Only you can answer that. If you have the money, consider what other improvements could be made and which are likely to give you the most pleasure.