2005 Roush motor swap with a 2009 GT

[05 ROUSH]

I swapped my 05 motor with an 09. I have done so much work to get it perfect but I continue to see this one issue. I have a random misfire code that moves randomly. Another note to add the motor came out of an automatic and was put into a standard.
-I am using a 09 4.6L motor in my 05 Roush
-I am using the 05 ECU and harness
-I have changed the coils and spark plugs for the 09
-I have changed the Fuel pump, fuel filter, fuel injectors, fuel rails, O2 sensors
-I have had the car tuned

I am running out of ideas, I have read that the 09 harness and ECU might be different and causing the random misfire. Does anyone know if this is the case.

 

[AHaze]

The '05 and '09 long blocks are functionally interchangeable.
Are the coils you installed Motorcraft for the 2009 engine? Early and late 3V coils are not interchangeable (have to match the cylinder head year) and aftermarket versions have a high failure rate. Which spark plugs did you install? Some brands are known to be problematic in 3Vs.
If you can eliminate those as possible causes, I would start the troubleshooting by checking all the grounds in the engine bay.