Well the big issue is the down stream oxygen sensors, the new electronics are 100s of x's faster that a lightning ever thought of being and with the O2s located further away the computer is expecting a certain reading for instance saying when cyl #7 is on the exhaust stroke and the exhaust is traveling further so it is not even close to correct in what it is reading throwing the PCM into total confusion. And in turn the PCM will throw the fuel system in and out of closed loop causing drivability issues. As far as a dyno tune, yes it can be done but 99% of the tunners out there are simply turning the downstream oxygen sensors off as if you had no cats and wanted to keep your ck engine light off. Whipple has dialed in the tune to function 100% with the long tubes. The guys turning the downstreams off are robbing you of power because the PCM is in a generic closed loop operation that never changes the fuel curves to match what the engine is demanding. Compared it to something we all know, its like owning a F150 that someone cloned into a raptor. Sure it looks nice and will do ok off road but the compared it to a real Raptor that does what it should. Why would you settle for less when you can have it all. Hope my explanation and analogy helps the understanding of header running issues.