2004 Explorer 4.6 manual trans swap... Problems with editor

I've swapped a manual trans into a 2004 Explorer 4.6. I'm having some problems getting it to run properly.
Setting the auto trans DTCs to "no error reported" prevents them from appearing, but the truck still goes into Failsafe Mode as soon as it starts to move. It seems as if the editor is preventing the faults from being reported, but the PCM is still taking action on the faults. I get a Failsafe Mode message and reduced power but no DTCs.
Setting the Automatic Trans switch to "disabled" (manual trans) causes a P0606 Processor Fault and Failsafe Mode immediately upon starting the engine.

Any suggestions?