Multiple codes/limp mode

Yes, a broken wire could definitely be the issue. If go back to page 1 I put all the diagrams up for you, I will post them here again, first picture is ECM powers and grounds, second picture is the DME relay, if those fuses have power the relay is working correctly.
Those fuses #F37, F39, AND F4 go to the DME.

Have you tried clearing the memory? I think it takes 30 minutes for the capacitor in the DME on a BMW to discharge fully. Try unhooking the battery for 30 minutes. You're sure you don't have any vacuum leaks, you can tell if you raise the RPMs and hold it, the idle hunting should go away if it's a vacuum leak.
But discharge the DME and recheck for codes.

Then you probably have a vacuum leak, but since you replaced the alternator, I think you should still clear the memory on the DME,
Now for vacuum leaks I'm leaving a guide below, but i usually try a spray bottle and water to begin with, while its running try spraying around the intake manifold gasket areas and vacuum lines. You'll hear it suck the water in when you're at the leak. If that doesn't work, you can follow the guide below. It's just safer to test with water first. It sounds like you have a big leak, so it should be too hard to find.
In a shop we use smoke machines to find leaks like this, but they can be expensive.

https://www.2carpros.com/articles/how-to-use-an-engine-vacuum-gauge

Okay, I do notice some things here, the first thing is, is this data while the car is at an idle? Just sitting still not driving, correct?
The next I notice, and this is strange, is that your rear 02 sensors short term fuel trims are reading 99% on both banks, but the actual fuel trim on pic 4 is reading 0, % actually they're all reading 0%, they should be reading something if the car is running, the system is saying open loop, so you defiantly should have some type of fuel trims. The fact that its reading 0 on all 4 is not good.
I'm posting some information on the p0091, I know this car has a High Pressure and a low-pressure fuel pump. Which is that reading of 1063psi, which seems low to me, but I cant find a spec for that. But you need special gauges to test the High-Pressure pump.
But here are some tech notes and precautions regarding this code.

The reason I asked about if you were driving while taking this data is that the VSS in picture 3 says you're doing almost 6MPH?

So, if you're getting a reading like that and not moving, plus now you're getting all these different codes, completely different from before except the cam codes.
I'm wondering if the high voltage of 15+volts damaged the DME (ECM). You're getting some crazy data here.
Not having any fuel trim numbers is bothering me to,
It's like the car has no control over certain systems.

Did you check the ECM powers and Grounds while its running?
I mean you didn't have a thermostat code before either. This is turning into a rabbit hole type diagnostic here. The p1417 code is Throttle Control Incorrect Air Supply, which goes alone with the p1636 code.

I would say that the High-Pressure Fuel pump should be checked because when they fail, because it's under such high pressure, they come apart and send pieces of the pump into the injectors, metal particles,
But you can't just put a regular fuel pressure gauge on there, 1,000PSI will do serious damage.

No, don't check the rail pressure unless you have the correct tools for that. If it's a high-pressure fuel system, it can be up 2,000-3,000-PSI in some cars. If there's no coolant in the car, that can cause it to hunt for an idle. Was that not checked before? Get the coolant filled and bleed the system and then run it, the coolant temperature sensor cannot read air, so the DME doesn't know where the fuel strategy should be. Fix that first. You have to make sure all the basics are okay first.

My concern was that the VSS (vehicle speed sensor is reading almost 6-MPH, but the car is not moving. Thats not good. Thats another error going on here. If the vehicle thinks it's moving but it's actually not, this will also cause Idle issues, because the data is not adding up in the DME (ECM). This another thing that needs to be addressed and find out why its reading 5.5-MPH. It doesn't matter if it's revving up and down, it still should read 0-MPH.

There's too many errors going on here to even start on a correct path for diagnostics, from my point here, this ECM should be fully checked, powers and grounds with a test light. Also checking the harness fully for any corroded connectors or melted wires.

Is your live data still reading anything on the VSS? And you checked for battery voltage at the DME itself?
Here's the actuator control diagram the black/violet wire is labelled Throttle Ground,
the blue wire should be a 5-volts or 12-volts reference.
Yellow and yellow/blue are the signal wires going to the DME for the Motor Actuator.
I'm not saying the DME is bad but you're still getting codes for voltage issues. You should also load test the Block Grounds and to the frame, using a 12-volt light bulb is good for load testing circuits. Just connect the lightbulb to battery positive and touch the other wire to the engine block and frame to verify with loaded circuit tests.

You can use a headlight type bulb for load testing, I already put the diagrams up for the DME twice already. Yes, those are the throttle actuator circuits. Here's the DME powers and Grounds again. On the third diagram, if all those fuses have power, then the DME relay is working.

Is the gauge for mph on the instrument cluster moving as well? It looks like the ECM takes data from the ABS module to calculate vehicle speed, this data is transferred via the CAN bus system. I wonder if you're having a network issue and that's why there's so many issues popping up randomly like this. Do you have a lab scope?
It's hard to tell exactly where this speed data comes from. BMW isn't very giving when it comes to system diagnostics. I'm still looking for more information
And are you able to scan the ABS module for codes or just the ECM?
And it's not just about the reading of mph at a standstill, you had voltage codes to begin with that you cleared. Replaced the alternator, now have different codes on two different occasions.
There's a bigger issue going on here, it's not just one sensor causing all this. You have got strange live data, vehicle speed without any actual, no fuel trim numbers, voltage codes for the throttle actuator, fuel pressure codes, cam sensor codes,
You may have to look at the CAN bus network to make sure modules are communicating with each other. There are way too many codes and odd data to give you any definite direction here.
When I see this much going on, there's usually an issue with main Ground connections or something to tie all this together.
Not just randomly shooting in the dark here. Did you check any voltage levels at the Throttle body?