I'm also thing about converting my game to Magna Mundi (2, when it comes out). This is how I plan to do it. Please note I have no previous experience with converting, and this is just wishful planning.
I don't intend to use the converter. I've seen some converted games and they look pretty messed up even in vanilla - don't want to see what it'd do with Magna Mundi with its special buildings, tech levels, cultures, country modifiers, etc. MM is much more detailed than CK, and I'm afraid I'd lose a lot of valuable data.
Instead, I plan to take the EUIII scenario editor, open the default Magna Mundi grand campaign (!) and edit it manually. To make it bearable, I won't edit anything else than existing countries, province ownership and perhaps religion. Other things (cultures, building, country sliders) will be kept as in Magna Mundi. My goal is to go through the map province after a province and assign them to new owners. If Magna Mundi doesn't have a particular country, I'll take the most similar unused one and rename it (eg. if I have Sultanate of Rum instead of Seljuk Turks in CK, I'd convert it to Ottoman Empire, and then rename it).
Feel free to say I'm naive and advise me against it
