What could be causing my 2009 Mazda BT-50 to misfire?

It sounds like you’ve tried pretty much everything here, but I have a few suggestions. Have you cleaned out the inlet manifold? The combination of soot and oil mist that gets recycled back through the Mazda’s engine (and a lot of modern turbo-diesels are the same) can cause all sorts of poor running conditions including surging and mis-firing. I know you said you’ve disconnected the EGR valve, but this build-up could already have occurred.

What about the fuel system? You said you’ve replaced the injectors, but have the fuel pumps been checked for flow and pressure? What about the fuel return line? Is it blocked and causing an obstruction to the fuel flow below 80km/h? What about the fuel pick-up inside the tank? A split or damaged pick-up can allow air into the system and cause all sorts of grief.

Also, this generation BT0-50 used throttle-by-wire. Many owners didn’t like the operation of the standard set-up and changed to an adjustable system that allowed them to soften (via a dial on the dashboard) the throttle action for off-road use. Has your vehicle been modified like this? Even if it hasn’t, the standard throttle set-up could be faulty and causing the problems you’re seeing.

The fact that the vehicle operates perfectly in some situations leads me to suspect an electronic or fuel supply problem. If it was a major mechanical issue such as a burned valve or a major mechanical glitch, the engine would likely not run properly at all.