The new engine is a TD42T and doesn't have any electronic control. The original ECU is just left where it was and is only used to run the trans. If the ECU is removed, the trans goes into limp mode - stays in 3rd gear.
My trans works exactly as before, I stick it in D and go..
I just removed any EFI related wiring that was no longer needed.
It won't interfere in any way with the Ford ECU.