I had a great local shop build a 340 stroker motor for me but I wanted stock carb and manifolds as it's going in an OE restoration. He broke the engine in using his favorite Holley carb and headers. After break-in the final numbers were 397 HP-465 TQ. After he swapped over to stock exhaust manifolds and thermoquad the final numbers were 395HP-443 TQ
I am willing to bet that you were using stock heads on this build and the reason your hp didn't change is because your heads are the biggest cork in engine. if you swapped heads to Edelbrocks or something similar and the redo the test you would see a very large difference between headers and manifolds. Stroker motors can push a lot of air at a lower RPM but you quickly find the limit of flow in the heads.
