I do it with the head piece off. If the piston is not right at the top of where the cylinder ends at TDC, you have to much space. The pistons have a crown and usually hit about 3/8" in from the outer edge. If the edge of the piston has .050" left before the top of the cyld, thats way to much space. You can put masking top in the head or on top the piston to see if its hitting when you get real close. If you try to mill the cylinder down you lose your o ring grooves. A thinner base gasket is the way to make the piston go higher. On my Polini there is no water going from the cases up thru the cylinder, but on a B1 got to have a good seal, so water don't leak at the base, don't know if Yamabond with no base gasket will probably work, its rubbery and seals pretty good.