You dont need to remove the motor to remove the head, cylinders, and pistons. If you have bottom end work to do, then by all means, remove the motor.
I never have thought about removing the cylinders with the head on, but again, why would you want to do that? Its going to have to come off to do any honing/boring, porting or head work...
Pay attention when youre putting it back together to make sure that head bolts are tightened in the correct order and to the correct torque in stages.
Just my $.02 worth. Your mileage may vary.