Another problem could be a faulty seal where the exhaust meets the head. If the person who installed the pipes didn't know enough to dig out the old gasket (or reused them) you may just have enough of a leak to cause the decel popping. All that you had done I would attach that next.
My '98 shadow has samson pipes and previously vance and hines classic II's and I did the rejetting and change over from stock - never once did I have to touch the idle mix screws, from how they were set (someone had taken caps out so they were adjusted at some point).
My fuel mileage is about as good as can be expected (mid/upper 40's) better than when it was stock. Absoulty no decel popping.