What do you mean by the water outlet doesn't line up with the holes in the cylinder? What holes & what cylinder? The water outlet is supposed to spray the water directly in to the inner bowl. If when it is filling the sound of the water is high pitched & sounds like it is straining then replace the water valve with a new one. This is quite a common fault where the inlet valve can't fully open.
Lincoln Appliance NZ, May 2009
