Where are you getting your ECUs? And are either of them from an '06? Highly unlikely you've gotten 2 bunk ECUs in a row but it's possible.
It might be that the fuel supply isn't available -- the secondaries could be firing, but 'dry'. I know you have replaced the fuel pump, and the ECU -- do you have a piggyback fuel management gizmo? PC III,or PC V, or BAZAZZ?Nobody?
By filter you mean air filter, right?I don't have any piggy back. Bike is all stock except exhaust and filter
The thing is I don't have the mod. Should I do it?Search the site for info on block off plates, and '05.... that should get you to pics and diagrams of what it should be set up like. My '09 is not the same layout, and has not been modified as far as I know.
Seems like the issue you are having is fairly common on those models, with the mod.