I think I would start looking at the slave cylinder/push rod end, especially as things initially seemed OK.
I'm not completely familiar with the 1200 set up, as my 600 has a cable, but make sure that there is no damage to the push rod, that the slave cylinder is releasing completely. You need to ensure that there is slack in the whole system once the clutch is fully released.
The only other suggestion is that you have insufficient clutch spring tension. Make sure you have the correct springs. If all else fails, you may be able to "preload" the existing springs with a washer to increase the pressure slightly.
Let us know what you find.