Just try starting in Neutral
Key on, foot on the brake, shift to Neutral, try to start
Assuming that since Ford looked at it there is no Flashing THEFT Light with key on?
So not a PATS issue
The DTR(range sensor) does have a physical switch inside that passes 12volts from Ignition switch, thru fuse 21 to Starter Relay in engine fuse box
So that switch could go bad
Computer does control Ground on starter relay, which is PATS issue
Manual trans NSS no longer passes voltage as Dirtman said, it just a sensor, clutch pedal down
2009 is same as 2008 wiring