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You can usually self check the MAF by completely disconnecting it. The engine should still run as the lambda probe will trim the fuelling to suit the emissions. The primary lambda probes are wideband and designed to control fuelling to ensure the engine doesn't run lean or rich. The secondary lambdas are not control they monitor for emissions. Assuming the lambdas were not switched round ,one possibility is that maybe you have a manifold leak on the block that is flexing when the engine is hot. I assume all the gaskets were replaced and the manifold (header) bolts torqued from the inside outwards ( ie the bolts at the ends of the headers are tightened last).
The only other case of rough running i've heard of is when the cross tee on the inlet manifold has become loose, this allows more air after the MAF to enter the engine causing a lean mixture. you could also check the hose clips on the inlet manifolds on the cross tees.
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