Hi
Had a similar problem with my solex it was the dome nuts which protruded into the bonnet, however I have recently changed to a 28/36 and find that it fits better as i am able to include the dome nuts, it may be the thicknes of the filter, mine is a D shape and only approx 20mm thick, unsure if you can get thinner ones, but have you replaced the insulation block to the manifold this may be thicker than required. try flat nuts if all else fails I know it does not look good but better than the bonnet not shutting.
Daniel Rance