New member. 4.6 3V standalone swap – starts and dies in 2 seconds

[chesk]

Hello everyone,
New in the forum.

I'm currently working on a standalone swap using a 2005 Mustang GT 4.6L 3V engine with the original manual transmission PCM, installed in a 1967 Mustang Fastback.
Since I couldn't find any reliable information on how to build a standalone harness for this engine, I simplified the original wiring harness following the same logic and methodology that Brendan from LT1Swap uses for GM LS engine swaps.
The project currently consists of:
Original 2005 Mustang GT PCM.
Original engine harness simplified for standalone operation.
Manual transmission.
Original engine sensors connected, including the MAF, FRPS, FPDM and all critical engine sensors.
FPDM connected and operating.
HP Tuners MPVI2 for reading and writing the calibration.
VCM Scanner for live data and diagnostics.
The standalone conversion has been successful in the sense that the engine starts immediately and runs well, but it shuts off after about 1–2 seconds every time.
The PATS delete was performed by a third-party service. However, since we didn't perform the modification ourselves, we cannot be completely certain that it was done correctly.
Most of the live data looks normal. The only value that seems suspicious is the Fuel Rail Pressure Relative reading, which stays around 9 psi.
The PCM is not storing many diagnostic trouble codes, which makes troubleshooting more difficult.
The vehicle does not have:
The original instrument cluster.
The original ignition key.
Any of the original body modules.
It is simply the engine, manual transmission, simplified standalone harness, and the original PCM.
The only DTCs we have found are:
P0685 – ECM/PCM Power Relay Control Circuit
P0690 – ECM/PCM Power Relay Sense Circuit High
P1000 – OBD Readiness Test Not Complete
Has anyone here successfully run a 2005 Mustang GT 4.6L 3V PCM as a true standalone?
If so, I'd really appreciate any advice. Could these DTCs be responsible for the engine shutting off after 1–2 seconds? Is there another module or circuit that the PCM absolutely requires to keep the engine running?
If you've successfully completed this swap, or have any wiring diagrams, HP Tuners experience, or troubleshooting ideas, I'd be extremely grateful for your help.
Thank you!

 

[Jonas1ne]

Welcome! It sounds like you've done a very thorough job simplifying the harness.
A couple of things come to mind:
A start-and-die-after-1–2-seconds condition is still one of the classic symptoms of PATS not being fully disabled. I'd verify the calibration with someone experienced in Ford PATS deletes before chasing too many other issues.
The P0685 and P0690 codes are worth investigating. If the PCM isn't seeing the PCM power relay circuit exactly as expected, it may not stay in its normal run state. I'd confirm the PCM relay control and relay sense wiring against the factory wiring diagrams.
A Fuel Rail Pressure Relative reading of around 9 psi seems suspicious. I'd compare that to the actual rail pressure with a mechanical gauge (or verify the FRPS signal and reference voltage) to make sure the PCM isn't seeing implausible fuel pressure.
Since you're using the original FPDM, I'd also verify that the fuel pump duty cycle remains active after startup and isn't being commanded off when the engine stalls.
Finally, check whether injector pulse and spark disappear at the moment the engine dies. That can quickly tell you whether the PCM is intentionally shutting the engine down or whether you're losing power, fuel, or ignition.
I'm interested to see what you find. There aren't many documented true standalone 2005–2006 4.6L 3V PCM swaps, so your findings could help a lot of people.
Goodluck