The 1200 will need some clearance for it to fit in the 1000 frame... it will also require some conversion to switch the bike over to a hydraulic clutch as well and some electrical modifications for the fuel pump and the ignition. Oh, and there is the output shaft of the engine to worry about as well. The 1200 does not use the circlip and the universal shaft is held onto the output shaft by spring pressure. The 1000 drive shaft does not have the spring, so you would need to have the circlip in place. The 1100 would need some electrical changes for the differences in the ignitions, but that is about it.
I like the 1200 motor better than the 1100 due to the hydraulic lifters. The torque that the 1200 has feels like it is more than the 1100 as well.