06 Z400 Magneto Stator Assy
 

See below

06 Z400 Rattleing in crankcase
 

Not sure what you are saying exactly.......

You mean you took off the bolts and could NOT get the case to budge? The clutch cover has a lot of bolts to take off including the water pump housing bolts which need to come off as well.

Not sure what could be "rolling around" in there..... Does the noise change if you pull in the clutch?

06 Z400 Rattleing in crankcase
 

UPDATE!:
I got the case off with some help and the rattiling was a bolt head from one of the bolts that hold the rotor Assy in place, 2 other were finger loose. The stator assy is a little chewed. I put it back together but now it wont run right it has a hard time starting and when it did it back fired once then poped in the air box, also the motor was shaking when running at one point it still did sound too good. I did try turning the engine manually with a wrench on the crank bolt, I think i maybe have messed with the timing some how. How do i fix this? do i need a new stator assy? what should i do next?

06 Z400 Rattleing in crankcase
 

see above