Since you mentioned the exhaust, I assume you mean it's backfiring out the exhaust, and not back up the intake.
Setting up true duals probably just made it so you could hear the backfire better....does it backfire on acceleration or deceleration? If it backfires when you take your foot off the gas, it could be a multitude of things, including even head-to-exhaust manifold gaskets.
On accelration and only acceleration. Its almost like its firing when the exhaust valves are open