97 Cobra Coyote swap Randomly won’t start

I have a 97 Cobra with a 2012 Coyote in it. The car is Lund Racing tuned and has the coyote control pack. It also has a return style fuel system. I just replaced the alternator due to the old one getting weak and not charging the battery.
As for the issue:The car runs great but every few days the startup seems a little weaker than usual and then it will end up cranking over a couple times then stop. Fuel pump will keep running and all accessories still work but won’t turn over and no clicking or anything to indicate low battery voltage. The battery voltage will still be around 13v and it still read 1000 CCA when tested (Optima Red Top). The only way to get it to crank and start is to disconnect the battery for 20 sec or so then hook it back up. When it does start again, it turns over a little more sluggish and takes a little longer to start. I have also notice that when the car warms up and is at idle, every now and then it will have a stutter like it’s going to die then pick back up. It has been showing a bank 1 cam retarded code so I’m not sure if that could be the cause of all this or if maybe it’s the tune or control pack. Any assistance on this issue is much appreciated.

Bump

So I will have to get back out there and look at a few more things. As an update, I replaced spark plugs and the cam retard code is no longer active. I discovered last night that once it does the not starting, my scan tool has an error saying it cannot connect to the vehicle. Disconnect the battery for 20 sec, reconnect and everything works fine again until the next random time it decides to not work. As for the alternator, it is a factory alternator for a 2001 mustang due to the PBH bracket kit only fitting that alternator. It is also reverse mounted. I bought the car already swapped so I’m still working my way through the whole thing to see how everything was done or if there are any sketchy wiring connections. I’ve been taking a look into the clutch safety switch because when it decides not to start, that’s what it seems like. Absolutely everything will work except starter.

Also the battery has been relocated to the trunk and I noticed the only ground coming off it goes to the body.

Bump

wmburns said:

To me this says, "no power to the PCM". Go back to basics. Check power(s) and Grounds to the PCM while the problem is happening. Focus on the ignition pilot duty circuit to be sure that it's working as intended. Note, no clue HOW this works for your project.

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so the distribution module for the coyote control pack was showing fuel pump on and power to the pcm with the ignition at the on position. When the key was turned to start, the light for start on the module did not light up. There is a ground from frame to motor as wmburns was asking. I unplugged one connector from the pcm for about 20 sec, plugged back in and the car started right up. Could this mean there is an issue within the pcm since the only way to start the car is by resetting the pcm?

The light for the pcm power does stay on during crank, just no light for start. It just baffles me because I can sit in my drive way and start it one minute, kill it, then go to start again and it will turn over a couple times then the starter acts dead. I’d say it’s on average around every tenth time that it won’t start. I wish my starter was easy access so I could run a few test on it without having to tear half the car apart.[/QUOTE]

wmburns said:

This says to me either:

The power for the PCM is supposed to be ON while the key is in "run" or "crank". What IF the PCM power is dropping as the key is turned to "crank"?

The PCM is never receiving a signal when the key is turned to "crank". It's well known that the PCM is expecting certain signals to arrive in a specific pattern. Perhaps this confuses the PCM such that it's waiting for a "crank" signal that never comes. Resetting power to the PCM resets the state of the PCM back to default.

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I’m going to see if I can get an extra set of hands and measure the actual voltage running to the pcm as the car is being cranked. My thought is The light is an led so wouldn’t take much to light it up even if the power is dropping below normal.