If i have a 96 PCM a 96 engine Harness on a 98 cobra and would that give me an issue. Currently my car will start but will shut off. Ive spoken to a guy that deletes PATS and he let me know that my symptoms are not PATS related.
There is a lot of misinformation on the internet about the fuel system in the 98 Cobras. It turns out that, other than a different set of baffles in the fuel tank, the fuel systems are identical from 96-98 Cobras.
There are a few minor wiring differences between the 96/97 vs 98 cars. For example, there are two pins swapped in the 98 instrument cluster harness compared to the 96/97 harness. You could be getting bit by a slight harness difference. The best way to do this project is to buy a 96 or 97 EVTM and a 98 EVTM on eBay and compare them.
But in the mean time, start with the basics. I assume you have checked all of the related fuses. With the key on, engine off, you should see 39 PSI of fuel pressure at the rail. It should not leak down for several minutes after you turn the key off either.
If you are not getting fuel pressure, make sure you are getting power to the fuel pump. Make sure the inertial cutoff switch hasn't been tripped as mentioned above. There is a 2 stage power supply that controls the fuel pump. At low RPMs, the fuel pump power is run through a resistor in the fender well as Shurur said above. You should see about 9V at the fuel pump if that resistor is there and working. If not, you need to check that resistor. Also check for power at that resistor. At higher RPMs, the PCM closes a relay that shorts that resistor out, sending full power to the fuel pump. That relay is somewhere under the dash, around the glove box, but I haven't been able to find it on my Cobra yet. That relay can't be the problem, because it only works at high RPMs.
FYI, if I remember correctly, the fuel pump relay is controlled by the PCM. If they key is on and the engine is off, the PCM will cut the power to the fuel pump so the fuel is not constantly running when the engine isn't. You need to be fast to see the power to the fuel pump when you turn the key on. It is useful to have someone turn the key on while you are watching your voltmeter to see the power come on and then go off.