Dan have you replaced the the 2 end pins with studs? They just unscrew with a vise grip. Replace them with studs long enough to allow you to add a lock washer and a nut. They are on the exhaust manifold ends and shouldn't be causing a vacuum leak but still a good thing to do. Are the bridges that span between the intake and exhaust flanges bearing down on both? It is possible for them to bear more on one flange than another either due to different flange thicknesses or deteriorated bridge pieces.
