Badger,
When removing the 16 x CAPPED NUTS from the studs to remove the cylinder head, the studs can sometimes loosen in the lower crankcases with the nut still tight on the top of the stud. This can sometimes be heard as a "screeching" sound as you first loosen the nut before it releases.
This can then result in those studs sitting slightly HIGHER than they should be, so I always put one of the CAPPED NUTS each stud and carefully tightening, to ensure the studs are fully seated and all the same length, before refitting the head.
If you DONT do this and some of the studs are higher then others, you will not be compressing the new cylinder head gasket as required on all 16 studs as the top of the nut inside reaches the top of the stud and stops, which can result in head gasket leakage.
Also, its worth applying a smear of grease to each side of the 16 washers below the nuts, so it does not "grip" its seat on the cylinder head when tightening the nuts to the correct torque setting.
This applies to any studs on most bikes with capped nuts on them.
Pete F
UK