Could the lack of contact of two inboard exhaust ports be caused by the intake manifold being a smidge too proud toward the head preventing the exhaust ports from sealing? If this is the case, maybe loosening the two bolts and two nuts that hold the intake to the exhaust together, then bolt it to the head without the gasket for the purpose of aligning the manifolds. Once the the hold down bolts are tight, tighten up the two nuts and two bolts. Use a thin feeler gauge to check for a good fit at the exhaust ports. If everything is flush, take the manifold assembly off and reinstall with the gaskets and check for leaks. A hose held to your ear works good for hearing exhaust leaks.
