C0539 the main thing to check is to verify the operation of the VCT solenoid. You're looking for a sticking or stuck VCt solenoid valve caused by contamination. Refer to vehicle specific repair manual to perform component tests for the VCT unit.
The rule of C0539 code when it comes to emissions-related vehicle repair is that any modification that changes the vehicle from a certified configuration to a non-certified configuration is considered tampering: this applies to both vehicle owners and repair facilities and is, therefore, a Federal offense. Replacing a catalyst with a straight pipe is one traditional example. Likewise, overriding the OBD 2 system through the use of high-tech defeat devices or non-certified computer chips, for example, would also be considered tampering. The OBD system may, however, be repaired back to its original certified configuration with certified performance chips or appropriate aftermarket parts.
The crank but won't start condition, along with the trouble codes may make you think you've got a PATS anti-theft system problem. However, Ford reports that these codes are all related to software bugs. The only way around the problem is to reprogram the PCM with the latest software.
Brake Switch Out of Self-Test Range Indicates that during Key On Engine Off (KOEO) Self-Test, BPP signal was high. Or during Key On Engine Running (KOER) Self -Test, the BPP signal did not cycle high and low. Open or short in (BPP) circuit Open or short in stoplamp circuits Damaged PCM Malfunction in module(s) connected to BPP circuit (Rear Electronic Module [REM] Windstar and LS6/LS8 and Lighting Control Module (LCM) Continental and Town Car) Damaged Brake Switch Misadjusted Brake Switch Check for proper function of stoplamps. Follow correct Self-Test procedures, refer to Section 2, Quick Test.