The "DE or XC" has been the black sheep of the GG family. It really could be any combination of parts that the customer wanted. That description should be fairly representative of the DE/XC bike. The DE/XC bike definitely would have the smaller flywheel with less lighting output (about 35W)... this is what we call the Kokusan 2K-2. The EC is a heavy flywheel with more lighting output (about 70W)... this is what we call the Kokusan 2K-3. The MC bike would have a small flywheel with no lighting coil... I think this is a Kokusan 2K-1 (if I recall correctly).
Regarding the MC ignition, some of the the DE/XC bikes had the MC CDI installed. Others may have kept the EC CDI. Also, the cylinder head for the DE/XC bikes often had the higher compression head of MC bikes. So yes, it is confusing to say the least.
The 2006 was a transitional year, you are probably right that the DE's ended in '06. How many were offered is questionable. The '07 bikes would have been more EC-based with a few DE-type bikes custom built from what I hear members discussing.