PCM problems?

Are there any labels on the fuse box cover on the inside? Fuse 23 powers up the ignition coil but if the PCM is not being fully powered up then you're going to be missing spark and fuel injector pulse. The check engine light should not be flashing either. The fuel pump is not controlled by a relay in this vehicle, it's powered directly from the TIPM. And if you're hearing relays clicking that is usually a sign there is low voltage to one or more of them. Are you sure your battery is even any good? Have you had it load tested? Batteries only last around 3 years now, they don't make anything to last anymore. If you were having battery issues before, it needs to be tested to see how low it drops. I'm not even sure what the original issue is here. You went from moving some harness around under the dash and getting the Chime and some power back briefly to the GPS box, and asking about a battery drain issue. You need to have the battery charged up, then load tested to see if it's any ground to begin with. If it holds 12.6volts at minimum overnight and doesn't drop down below 9.5v to 10volts during a load or cranking test, then you move on to checking the powers and grounds, but this is just all over the place. Charge the battery overnight or replace it.
Also, the codes you had in the PCM were not from the old PCM, Codes that were in the old PCM do not transfer over to a new computer, you probably didn't even need a new PCM. This sounds like a low voltage issue, which is where you need to start, not just replacing parts. Start with the battery, if there are still low voltage issues then check inputs and outputs of the TIPM.
Low voltage is probably what caused the U1120 code as well, it's a PCM not receiving a speed signal over the CAN bus network from the ABS module. The PCM doesn't have anything to relearn in order to start, These TIPMs are known failure items, but you have to know if the battery can handle the load and doesn't have any shorted cells inside.

https://www.2carpros.com/articles/car-battery-load-test

https://www.2carpros.com/articles/how-to-charge-your-car-battery

Okay, so the number 1 fuse, is this a Convertible model? I see a number 1 fuse 40Amp, and just so you know, I have seen these vehicles with a ton of electrical problems, So I don't think this is a PCM issue, but if this was the Fuse 1 40amp that was popping, let me know, it's also possible the GPS box was causing a drain. The power and ground wires to that box should have a plug that can be unplugged from the box for now to eliminate that from this issue.
But let me know if this is a convertible or not, just because it's not popping that fuse right now, doesn't rule out a wiring issue, the wiring harness moves and vibrates while you're driving and short circuits can come and go, as for right now the vehicle has been sitting. What's going on with the security light, is it staying on right now?
Its really strange that the mechanic wouldn't give you the codes, that to me points to someone who might be trying to take advantage of you. I have seen mechanics leave ignition coils unplugged under intake manifolds, and other strange stuff that can't happen by itself, so it might be that he was just trying to get more money out of you. I have quit working for shops because of that reason before.
And with all these PCMs being replaced where they programmed by someone? Each new computer needs to be programmed to the VIN of the vehicle or it won't start. If the security light is staying on, that might be why. It takes a higher end scan tool to program PCMs. You can't just plug one in and it will work.

If the theft light is staying on then the security system is activated. The MIL light shouldn't be blinking either, it should come on for about 30sec at key on then go off. This might be an issue with not having the key Fob, you said you only have the grey key so that is probably why it is not allowing you to start. Service info here is telling me that the VTA (Vehicle Theft Alarm) senses when the Battery has been disconnected or failed (low voltage) once reconnected the VTA enters power-up mode, and the Alarm system remains armed. So, it might be the Theft system is causing the no start issue. Service info is also stating that the Theft light flashing you are seeing is the system arming itself. I can't explain why it would be doing this, some of the information here is aftermarket. So, it doesn't give everything, but it does say to disarm the Theft system " a valid Sentry Key Immobilizer System (SKIS) key" must be used. So, I don't know if there is a chip or the correct chip in the grey key you have. But the light blinking and then staying on looks like its arming itself. That would also explain the no spark.
You can try to disable the system; we do have a guide for this. It might work, it might not. But give it a try. You might need to have a couple new key fobs programmed to the vehicle. A locksmith can do this. They have the equipment required for it now. If a programmed key Fob doesn't get it started, at least we will know the Theft system is disarmed.
He will also have a scan tool that can probably tell if the Theft system live data PID says Armed or Not. An advanced scan tool could tell what the different modules are doing. It should be able to tell if there is a key in the ignition switch as well as the status, such as crank, or run.
What's odd to me is that power for Fuses 23,26 and 32 all come from the ASD relay being activated. Which means the relay has to be working, but power to the Sentry Key (security system) comes directly from the TIPM. So, the ASD relay might be working but starting is being inhibited still by the security system. Flagship One is a company that sells remained modules, and they offer modules that can have the security system disabled, but it is expensive. So, I would try having some new keys programmed and see if that helps. You need more than a Valet key anyway.

https://www.2carpros.com/articles/how-to-reset-a-security-system

You just wrote the theft light comes on and blinks then stays on. The theft and immobilizer are both security measures.

Okay, I went back over the first couple pages of posts, in one of them you had stated you moved some section of harness around below the ignition switch and had some power come back. Diagrams 2, 3 below are the OEM wiring diagrams, so let's check that power is coming through the Ignition Switch. Diagrams 5, 6 are looking at the Ignition switch connector, so when you look at it plugged in, you'll be looking at it from the back side. Most of the time these connectors are not weather pack with seals, so you should be able to use a multimeter to check the ignition switch plugged in. Since you're only getting a reaction in the Start position, pin 3 might not have voltage coming out. Pin 3 goes to the label output B, which goes to diagram 4 to specific modules.

If moving the ignition switch wires around is affecting the security light then you have a connection issue, there's a number of reasons he couldn't program a key, either the key is bad. Which he should have programmed a new key to begin with. Or the power is not waking up modules, you need to make sure all the pins for the ignition switch connector are tight, any loose connectors are not going to help anything, especially the ignition switch.
Here's both OEM and aftermarket starting circuits. But the clue here is the change in the security light, I understand this is frustrating, but start with the basics, you know there's a problem with the ignition switch connector. I would even put the old PCM back in, who knows if it's programmed to the correct VIN right now.

It wouldn't be "locked up" with a properly programmed vin, you said you moved the wiring under the dash, and it had an effect on the cluster, so there is a wiring issue there for one. And if you're buying remanufactured cheap PCMs from AutoZone or some place like that, you might not even be getting a decent PCM, most of the time they just repaint them and sell them again. I would concentrate on the wiring under the dash instead of throwing parts at it, you're just going to waste money. You need a scan tool that can tell you if the PCM is seeing the correct inputs from the ignition switch, so buy a decent scan tool that can read live engine data as well as other modules before buying more components. But an Autel MX808, they are a lower end Autel but they can read every module in the vehicle. You can get one for less than $400 right now.