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.

What the car is at a NAPA auto care, and they still can’t diagnose the problem it’s been there 3 days.

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.

This is what it’s doing and all it’s doing.

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.

And this is how my dash looks and I’m not sure what tests they’ve ran they keep saying they haven’t found anything yet but believe it is a connection issue.

Won’t be able to get up there to check again until Monday.

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.

Yes, some kind of surge happened during that alternator swap out I most definitely agree.

Car fixed it was missing fuel pump fuse and some fuses were misplaced so now it drives smoothly but there’s a winning noise underneath my hood and it’s sluggish on take-off only when gas tank is almost one like so. I put some premium gas in it was running cool just now filled it up still a whining noise and my air doesn’t work now. However, when I try to do a fast take off my car shakes and shutters .

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?

Yes. You think the blower motor is damaged?

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

Yes.

And the condenser turns on but no air comes out.

Someone suggested blower motor resistor relay.

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.

I believe I got it figured out, but I’ve been having trouble with my car switching gears my 3 gear will get stuck and a certain RPM sometimes I have to change it manually, but I just left the shop my good friend put it on his machine, and it said something about a speed sensor. any idea on that?

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.

Yes, it was the HVAC system. So, I should change my TCM or the sensors? And yes, this car has a lot more problems than before but I’m willing to learn but I also can’t give up on this car yet unfortunately. But on take-off my gears stick my car stalls a little then it kind of catches itself back up to speed a little but if I’m going 40 MPH it doesn’t feel like 40 lol it feels like 30 MPH.

No don't just change parts, if your friend has a scan tool, have him monitor the speed sensors while driving to see if they are outputting the correct data. Do a full system scan, every module for codes.

Here’s what it’s doing you can hear the noise as I’m taking off and the stress it only happens like this when gas is below half.

I can see the Check engine light is on, what codes are stored in the ECM? I can't hear anything in the video, I would need to be in the car to hear it, but the ECM is setting a code, I'm sure that will give you direction, write down the code number, and I'll look up the criteria for you.
Just stop by AutoZone or another parts store and they will scan the car for free, just get the code number, don't let them sell you any parts yet.

My car is stuck in limp mode and got off the phone with a guy in a transmission shop. He said my conductor plate that’s why my speed sensor isn’t responding. But nobody works on transmissions anymore, but I have lost some transmission fluid, but he said the cost and labor of that plus new fluid is about $1,000 but most shops are recommending me to Dodge.

Conductor plate? Thats a new one. What codes are set in the PCM? Are you getting an "Output Shaft Speed sensor", Input shaft speed sensor, wheel speed sensor, vehicle speed sensor, code? I don't see how a transmission guy can tell you what's wrong without even scanning or looking at the vehicle. There is more than one speed sensor in the vehicle, service info states your vehicle gets its vehicle speed reading through the BCM on the CANbus network from either the PCM, ABS/ESP module. So, it depends on what actual code is being set to diagnose the system. Limp mode is a safety mode.

He said the sensor that’s in my transmission and that’s what pops up on the engine scan tool was “speed sensor”. I just can’t remember the code and I can’t move the car because it is in limp mode. I have a Mercedes transmission.

Transmission output sensor and I’m low on fluid.

Is it the 8HP45, 845RE or the NAG1? The first two Automatic Transmissions have 8 gears plus Reverse, the NAG1 has 5 plus Reverse. There are quite a few different setups with each transmission as well. There's a lot of information here, do you know if it's the 5 gear or 8?
Is there one bulk connector on the transmission? Maybe we can check the harness for any issues, On the 8-speed transmission the Output shaft speed sensor looks to be bolted into the valve body, all information transmitted to the transmission and back to the TCM is done mostly by a CANbus network. We can verify the Transmission Relay and fuse that power up the TCM, but this still depends on which transmission we're dealing with. The 5 speed has a smaller connector
With the NAG1 Tranny it states that there is no speed sensor internal to the transmission that directly measures output shaft speed, the ABS wheel sensors provide the output shaft speed.
So, did that code come from the ABS/EBCM module or was it from the TCM?
Is it possible we're dealing with a bad wheel speed sensor?

This is the OSS for the 8 speed transmission, it appears to be under the valve body, but its not clear if the sensor can be replaced without removing the valve body.

It’s a 5-speed transmission, so it may just be the ABS wheel speed sensor.

Okay, this is a really complex transmission. If there is a speed sensor fault, the code should also be stored in the ABS module, if it is, that at least will give us some direction here. For a 2wd, there are wheel speed sensors for each tire, one in each hub, sometimes the trigger wheel for the sensor is built into the wheel bearing. You can start by checking that the wiring to each sensor is not damaged. Service info doesn't say what type of sensors these are, there are some different codes for them though, and a flow chart for testing, but it would help if there was a code for a specific wheel. There is most likely some reference current or voltage monitored for it to be able to set these different circuit faults.
Is the ABS light on? Because it looks like the only other output shaft speed sensor is for the other transmission type. We really need more information on the code that was set. Without it, it's just assuming. If you can get the code number from your friend, we can then see what the code setting criteria is for it.

Sounds good, I’ll check back in with you in a few.