I would remove the manifolds, scrape the head and manifold surfaces clean, separate the intake from the exhaust, and remove that gasket and clean those surfaces.
You need to free up the stuck flapper, it is important that it functions properly.
Once everything is apart, clean and functional, you will want to put the intake and exhaust back together with a new gasket and leave the bolts/nuts loose.
Now install the intake/exhaust manifold assembly to the head WITHOUT gaskets and tighten the manifold-to-head bolts to specifications. Make sure that you have the three alignment rings.
Now is the time to tighter the bolt/nuts which hold the intake to the exhaust manifold. This will ensure that the two manifolds align with the head surface.
Now take a thin feeler gauge and try to find any gaps between the manifolds and the head.
If there are no major gaps, remove the manifold assembly and install the gaskets and drive it like you stole it (from a really slow person).
If there are significant gaps, put a straight edge on the manifold assembly and on the head to see where the problem is.
Carl
