Engine Crank no start 99 gt 4.6l supercharged. Advice needed

Hi,
Do you have a dongle or tuning device with a copy of the modified tune the EEC’s running ?
Have you verified no spark at the Coil?
EEC failure is rare, more likely wiring, or power supplying it. Do a thorough check of your electrical system.
Check the ground(s) from the battery terminal to your EEC, Chassis, b-leave the.terminal(S) disconnected for an hour or so while carefully searching for and correcting shorted wires, melted wires, substandard or corroded terminations. Pull apart plugs & the covers on all your fuse blocks &
look for water entry, or corrosion, fuses.
Use an ohmmeter and look for any low resistance paths from the positive cable to chassis ground.
Check your battery voltage. Should have 12.5V+ at the terminals, disconnect both terminals & put it on a low charge setting while you’re cleaning & checking things. If voltage is very low, bring it to get load tested. Check your Alternator wiring, and it’s power wire to the battery, corrosion on the plug, etc..
The fact is your EEC is unable to complete it’s self (readiness) check due to self-fault may only be a poor ground, shorted connections, melted wires, pulling the voltage down too low for the EEC to function properly. Has it been running typically of late?
You mentioned the security system (PATS). Was your security light flashing randomly previous to this, or now & how recently did you have the last issue mentioned? If you have another Key, try it. A decent Scantool should be able to see the EEC code thrown from this.
Good luck!
-John

Hi,
I apologize, should’ve clarified, whether a twin screw, roots, centrifugal FI, limited access won’t prevent access to any of the ignition & Fuel
Since this is a ”Crank, no start” issue, with the EEC indicat potential issues, focusing on the (2) points below in order to establish baseline info. EEC’s fail, but fairly atypical. This Testing will narrow things down, considerably.
~~>Ignition. Correct input to Coils. Pulsed ground trigger from EEC. Correct spark timing..**
~~>Fuel system. Presence, Pressure & flow. Pulse from EEC. Correct injector timing. **
IGNITION:
If you, a friend has a known functional, spare COP, and a spark tester or plug....
1) Pull a COP’s input plug & plug it into the known functional spare with a Spark tester or plug inserted, ground to the block. Have a helper turn it over. Should see a spark. Try a few of them. OR...
Multimeter & a NOID light..
A) Using a NOID light, you should see cyclic ground pulses occurring as light pulses as the engine is being turned over. Then, with a VOM on DCV, test the Voltage inside the connectors with the key On, should be 12VDC.
FUEL SYSTEM:
2) Using a NOID light, test a few (2) pin injector’s plugs as the engine’s being turned over. You should see a flashing light. Then, With a VOM on DCV, 12VDC should be present across the terminals with key On. Try a few, if ok- we’ll move on.
— The pump’s priming as it was previously, you mentioned you’ve taken care of that?
—BTW, L & R rear Areas where Windings seem slightly discolored within Alternator, may be the Pic’s, or misinterpretation on my part.(?)..
.—Just in case the EEC’s in need of a Reflash or replacement, do you have the program the EEC’s been running on a Dongle, Tuner?
—Is your Scantool capable of viewing PID’s (stream live EEC data onscreen), drive cycles, freeze frame, etc
Any questions about anything I’d posted, or if you’re unsure about a process I’d listed, ask away!
God luck
-John