Starting issue?

Hello, that is absolutely the incorrect way to disconnect a power source on a vehicle, I agree with you, I have no idea why he would not unhook the negative first and leave it unhooked. Then disconnect the Alternator positive post. Have you done through all the fuses in the vehicle? Did he leave both positive and negative cables hooked up to the battery while replacing the Alternator? I will look up the wiring diagrams for your vehicle and see which circuits could have been affected. But I wouldn't go to him again, and really if there is damage to any modules, he is responsible.
I remember this vehicle's charging issues from last month.

There is a fuse (Fuse 35 10amp) in the rear fuse panel that goes to the Intelligent Battery Sensor (current sensor) which communicates on a Lin Bus network to other modules. These sensors are extremely fragile. And most of them have a bolt on them that is a onetime use, but doesn't need to be disconnected because it's not the hold down bolt for the battery post,
But if you saw sparks flying while this guy was changing the Alternator, that's not good. Now you have starting issues. Does the Check Engine Light come on if you turn the key to just the on (run) position? Engine not running.
It sounds like something is going on with the security system. A start and then 2 second stall might be the security system not allowing access.

Which connector did he unplug from the fuse panel? Was it just a main thick battery cable bolted on, or was it a plug in connector type?
Was this the cable circled in the 2nd diagram?

Ok I found the Front Power Distribution panel with the main Battery positive cable running to it. The only issue here is that this is not the only place this positive cable is hooked up to, you'll notice on the 4th wiring diagram that positive battery cable runs to the rear power bus bar as well. So, he shorted out the main battery cable, not knowing it runs to another power distribution center in the rear of the vehicle. So, we need to figure out what is shutting down the PCM.
The 5th diagram is the Security System operation and I'm thinking about that Battery current sensor, and if it is possibly damaged due to the electrical arcing. The battery current sensor communicates on a Lin Bus network which is also the network that the Keyless Ignition system node communicates on to other important modules, BCM, PCM, IPC, and if the battery sensor happens to be pulling that network down, essentially shorting it to Ground because it's on the negative battery post. It would prevent a lot of things from functioning properly. This is just a hypothesis, since I'm not at the vehicle. But seeing if the vehicle is losing its Fuel Injector pulse after start up, would point to an issue like that. With the PCM shutting down the injectors.

Do they know about the power distribution center in the rear of the vehicle? Because with the front one unbolted like the mechanic did, the other power supply was still hooked up in the rear. They need to verify the power back there. Because those fuses feed the ASD Relay, and the Auto ShutDown Relay powers a section of the PCM, the fuel injectors, they might not have even looked in the rear of the vehicle yet, it's not a normal place for a fuse panel.
Ask them if they have power to the Fuel Injectors when the stall out occurs, or if they are losing Fuel Injector control at that time too.
It's still doing the start for 2 seconds then stall out, correct.

That engine almost sounds like it doesn't have any compression. Can you open the hood and do that again? Did the Napa place check for Ignition spark or fuel injector pulse? What testing did they do? And I'm not sure, but do you see any Check Engine light while cranking?
Also, I do not see the Tachometer moving while cranking.

They need to determine if the ECM is pulsing the fuel injectors and see if it has spark, those are the 2 first basic checks for a crank no start situation. If there is no spark, but there is still a fuel injector pulse, the engine could be getting flooded out with gas. That will cause cylinder wash and lower compression. I know you hear some type of rubbing noise while cranking, I heard it too, but let's figure out the no start first, ask them if they checked the rear power distribution center and its fuses. I saw the check engine light on, so that means the ECM is being powered up, but something happened during that Alternator change out.

Try adding a can of dry gas when you fill up next, there's probably some water in the bottom of the gas tank. Most gas stations have around 10 percent alcohol content in the fuel they sell. And if there's any water from condensation in the bottom of the tank, the water and alcohol will mix and stay together at the bottom of the tank because they are heavier than gasoline.
As for the noise. It can be a number of things, you can try taking off the main drive belt and see if the noise disappears, if it does then it's coming from one of the pulleys or whatever components are driven by that belt.
It sounds like there are still some modules in the vehicle that are offline, not sure how fuses got misplaced. Do you need diagrams for the Blower motor since you have no HVAC now?

Probably not the blower motor, but the HVAC control module might not be powered up. Are the LEDs on the head unit working?

Do you mean the A/C compressor comes on? I would check for power at the blower motor before replacing anything. This vehicle has a Blower motor power module, and there are 2 wires that run to the blower from the power module, the power module is not a resistor, and doesn't function like the older conventional blower motor resistors, It is a pulse width modulated controller, meaning it pulses the power to the blower to control it for different speeds, so depending on the duty cycle, that will determine the speed. With it not working there is probably a code stored in the HVAC control module that will lead you to the issue, instead of just replacing parts, if there's a shorted circuit somewhere and you replace the blower power module it might fry the new module and not fix the real issue. Because of how all this started I would be cautious about shorted circuits and/or more burned fuses. There are also input sensors to the HVAC control module that might prevent it from operating correctly. There is an in-car temp sensor, humidity sensor, sun sensor ambient temp sensor, evap temperature sensor, etc. So, scanning the heater controls would help, there should be codes set. Really doing a full system scan would be a good idea to see if any other modules are setting codes.

Diagrams 3, 4 and 5, 6 and 7, 8 are the HVAC system, you can see how complicated it is
The blower motor power module is 137 dollars alone, so it's not something you want to guess with.

What was the issue with the HVAC system? The output speed sensor reads the output shaft speed, and there is a warning on the TCM (transmission control module) being extremely sensitive to electrostatic discharge, which is exactly what happened when the Alternator was changed without disconnecting the electrical connectors. That incident caused a lot of problems, the speed sensors are hall effect sensors, so they are susceptible to voltage spikes.