Fitting the exhaust manifold on a Ruddertwin has been problematic for me every time, from the A to the J. And that includes motors I knew to be all original, not a mix of parts from different motors.
Most of the ones I’ve worked on had some kind of gasket in all three manifold openings. I had to use material of different thicknesses to get the screw holes to line up in the manifold, leg, and cylinders. Be patient, and try not to enlarge the screw holes in the manifold to get it to fit. Keep the cylinder bolts loose until you’ve got the manifold lined up with everything, so you can rotate the cylinders a bit. You may even have to adjust the thickness of the gaskets used at the base of the cylinders to get the screw holes to line up with the manifold. Best to dry fit all of this before you use any sealer, if that’s what you plan to do. The cylinder gaskets can probably just be greased. But if you use any kind of paper for the manifold, you’ll probably need some kind of sealer to keep them from blowing out.
Tom