Many headers are optimized for power, I think that getting one made to low rpm torque could be worth to consider, of course rest of motor must then match to that, so new program to ECU might unleash the potential of new manifold, but intake manifold can't be ignored either, depending what kind manifold that is, bit longer runners should help to get again more potential out from motor, then one likes to replace camshaft to offer better low rpm torque, but depending from original exhaust manifold type, it may be very good place to start.
It varies case by case. Good thing is that modern ECU units can adapt quite well, with knock sensor they can advance timing in certain window, putting new program then enlarges that window, it is not very easy to say when to chip as there are quite many variables.
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