Is it reading the TPS sensor properly? you might have a lazy TPS so the ECM isn't seeing the quick change in throttle position and going into "acceleration enrichment" mode. Or your MAP sensor is lazy or not working right, It could be that the stroker engine is pulling enough vacuum at part throttle that it won't fall into the enrichment tables in the tuning, why the WOT run takes that long to enrich is beyond me other than the ECM not seeing the WOT throttle condition on the TPS sensor.