My sons 6.4 cracked a piston last January 2021. We made a decision to rebuild the motor and at 19 I thought it would be a good learning curve as all we have worked on was a 6.7 and a 7.3. Well it has been a learning curve for sure. We did exactly that: rebuilt the motor and after machining and DDPM stage 2 rebuild kit and many deletes it turned out good.
Minor list of the build:
DDPM stage 2 with stage 2 CAM and matched springs, New Kill Devil Oring heads, ARP studs and pretty much ARP everywhere you can buy them, single turbo and dual fuel, 250 GPH FASS, Billet water pump, new remote fuel cooler (deleted one on t he motor), regulated return and the list goes on.
The truck has a Titan aftermarket auto/remote start feature that my son always wanted to remove or update so somewhere along the line as the truck cab sat he disconnected it to and had intentions on replacing it. We got everything back together and loaded it with 2 fully charged new batteries. All grounds cleaned and ready to start. All lights came on in the truck but ANTI theft lights flashing rapid, truck changed to Km when it was miles (number is there - no dashes) and just a bout every alarm you can think of is present. I have Forscan so I instantly tried to communicate to the truck. That did not happen so grabbed my hand held and that didn't happen. No communication. I checked all fuses and determined Fuse 70, 72, 74 and that line of fuses had no power. Dug up a simple diagram and found that those fuses are fed from Relay 53 (diesel). Pulled the relay and tested it. Works fine. So basically I follow that circuit and the ECM determined when to energize relay 53. Stuck now because I cannot communicate to it.

I did measure the OBD2 port voltage and found 12+ volts between 4-16 as well as 5-16. about 2.4V from 4&5-14, 4&5-11 and 4&5-6. Somewhere along my troubleshooting in previous years with other Ford trucks this was the voltage to look for.... 2.4V. So I'm guessing the truck is thinking it's stolen and I have tried the key on 15 minute X3 trick etc but none of those tricks work. His keyfob and panic does not work but his door locks do as well as his code on the door. Not sure how Ford scanners work and we did make an appointment for it at Ford so we can move past this point but obviously I'm towing it and NO I do not want them to try and start it but I have to crank it over. So the no crank no start ford blues have set in.
So you now need a question: What logic activates relay 53? Does the active Anti-theft have anything to do with the OBD2 port not working or deactivation of relay 53 so all communications between modules are down (not talking)?

I keep telling myself this is a ground problem but I also think its this PATS or anti-theft being active that has to be resolved first or I'm not able to go any further. The truck has been without power for so long that it simply lost memory of the keycode and now his key wont work? He has 1 key..... I know but at 19 I feel he needs a minimum of 5 at all times. Anyone able to help me get past this venture in the project?

 

Pats will cause a no crank (and possibliy a crank but no start depending on situation). I don't believe pats is causing the issues you have. Make sure the pcm is plugged in properly, check the connections at the smart module as this controls a lot of what you are describing. Smart module is behind passenger front kick panel. Battery disconnection should not have caused any pats issues but the fact you removed a remote start feature tells me that your issues will be found there. The remote start would have a relay on the ignition starter wire most likely under dash. If that relay isn't activated then you won't get any cranking. It may also be the source of your lack of voltage to other components. Start there first. Make sure that all relays from the starter system have been removed and truck wiring put back to original configuration. Sending to a dealer will create a lot of diagnosing time and possibly a very huge repair bill.

Edit to add: It's also possible that there is a coil installed at the ignition lock cylinder that mimics a key so the pats will work with the remote start. You will want to remove that if its there also.

 

To be fair the story in detail is that when we reassembled, everything got put back together and that batteries installed. At that point I knew nothing about a remote start (he knew it was there but didn't tell me). All the connectors were flushed out with electronic cleaner (including all the smart box wiring before batteries were installed) and dielectric grease added for all electrical connections. When it was all assembled, I had no communications and the PATS was active. My son went home and I continued. It was then that I noticed a bunch of wiring under the dash just hanging down as if a module was removed. I sent him a photo of it and he said OHHHH ya I removed that smart start because I want to replace it. It's somewhere in the truck. Further interrogation with him led to this remote start device and yes attached to the steering column behind the front removable dash plate was a box. I found ancient information about how to reset the little box and program a key. No luck. The point is we tried to put the key in and turn the motor over while the main Titan box below was remove which almost assuredly has something to do with my bad experience here. We then installed the box and went through the procedure of adding a key. Still not ok.
I'm going to follow your direction here and just remove the whole aftermarket system. Not a fan (especially now). Get the truck back to stock and go from there (not that the motor is stock in any fashion) but way easier to troubleshoot. I will remove all that wiring and check the smart box wire connections and harness tomorrow. I will let you know how it goes. Thanks for the help. Doing this is better than doing what I hate most...... Letting Ford figure it out for me $3k later.