Multiple codes/limp mode

That DME relay code came back, did you have battery voltage at those fuses that are fed by the DME relay? With negative lead on the battery negative? If that relay is not being powered up, or if there is a voltage drop across the relay and there isn't full battery voltage getting to the DME then of course nothing else is going to be getting full power either.
Check fuse F70 also for full battery voltage.
Also, if you pull the DME relay out, there should be 1 pin in the relay socket that has battery power all the time. The 2E85 also is not good, that's a communications code. The coolant pump is either missing voltage or its too low for the pump. This car is having voltage issues. Since you have no blown fuses that you can see, which I would recheck all of them, I'd say it's not a short to ground, but there's definitely a voltage problem. What was the reading on the DME voltage from battery? You wouldn't have this many codes without a main major issue. There aren't 10 different sensors gone bad at once.
You have to investigate source voltage issues here. Even if a fuse isn't blown, they do get hot and can slow current flow. If the terminals on a fuse are dark and burnt replace it. And go to the DME relay and check it there for battery voltage.

And what did you have at the throttle actuator for voltage readings?

To check the CANBUS network usually you would use a lab scope, but you can check the voltage readings, but this car, like all others, has multiple CAN networks. It's a 2 wire BUS that will have the two wires twisted together and when nothing is being transmitted both lines will be 2.5 volts, but when data packets are being transferred, the CAN HIGH will go to 3.5v and CAN LOW will go to 1.5v roughly. But I think you're dealing with more of a low system voltage. I don't see how you can have so many codes that keep changing as well as a code for the main relay that powers the ECM without low system voltage.
Just added 2EF5, is another code saying low voltage, 5 pic.

Since this has been the trouble car of the week for me, I haven't stopped things about this thing, I did some more investigating, and the 3100 Code can be caused by a bad Cam or crank Sensor or part of the Vanos system that controls cam timing, The 3100 is a boost deactivation code. The ECM does this due to a cam sensor or variable control solenoid issue.
The 29E2 and 29F3 codes are both for the Fuel Rail Pressure sensor circuit A, or signal back to the ECM.

The DME relay code 2ACB is related to the relay switching too slow or lagging behind and can set throttle related codes. Posting this below, maybe replacing this DME relay might be worth a try. Though I don't to throw parts at a car, at this point it's worth a try, relays don't cost much.

Also here, this may be caused by the DME relay not disengaging due to melted wires, so it can't turn off, the DME monitors this circuit and flags this code for possibly not shutting down.

So, the 3100 is not necessarily a fault, it can be due to a different fault. I will keep adding to this as I find new information tonight.
Also, I found out that the brake pad warning light should be on with the ABS codes. Not sure if it is or not.
Another thing, since you replaced the alternator, I was advised by a tech who teaches now, that the over voltage of 15.5v for a prolonged time may have damaged the battery.
More to come as I find info.

Okay, I have now gone through every code, the interesting part ive noticed is most of these codes are not present at the time of this reading. Except intake and exhaust cam sensors- DME relay- and low fuel pressure sensor (so this code is referring to the low-pressure side fuel system since this car has both low and high pressure.

I found something, this one circuit feeds everything you're having codes for. Check this out, second diagram, all power feed for everything you're having codes for comes from this fuse F37, and that's fed directly by the DME relay. I think this might your issue. It may be an intermittent problem which is why the codes are not all present right now. This maybe a low power (voltage) issue at starts up or something along those lines.

Thats what I was wondering too, I know if it's made in a different country, or from California it will have different emissions standards. But it might be the low-pressure side fuel system effecting the High-pressure pump, you can test the low side, it should be 72PSI, but the High side you have to be very careful with.
The DME relay is under the passenger side dash in the junction box. It will be in with all these fuses. Below.
I see you're using a different scan tool, can you get any fuel trim numbers with that?

What are the max the fuel trims are hitting and on short term or long term?
Oh, my goodness look at that fuse box. Ugly.
Try looking up the part number, that relay is upside down, so it's 19262.

Okay, I'd like to see the fuel trim numbers and whatever data is readable on that same screen. I will try to get a better location for the relay, its reading that its soldered on the backside of this box just above that black relay.

What was the other scan tool you were using before, the grey screen?
Those High Side pressure readings were down in the 100s. That scan tool doesn't do Fuel Trim numbers? Short Term, Long Term? It sounds really hard to start too. I think you're dealing with multiple problems.
When and how did all this start? Did you buy this at auction or something?

Hang on, there's a recall for that fuse panel I think, let me get this info.
There's also info on the main battery feed into that junction box behind the glove box overheating. You may be able to get the dealership to replace that fuse panel. Because it looks like you have to solder a new DME relay in, which sounds completely unreasonable considering how many problems they cause.

Okay, it looks like this is a smart junction box, there's some programming involved if its replaced. I couldn't find much on that, but I will give you what I did find. I would think it would be easier to replace the whole box if the relay is soldered in, but you'll have to see when you get it out of there. This is for the box behind the glovebox. That idle issue may just be the High-Pressure pump failing and leaking pressure back into the low-pressure side. I've heard of that happening. That might explain why the low side pressure was all over the place. I saw it hitting 90psi at some points.
If the High-pressure pump failed though, they usually break, and pieces go into the injectors. Small particles of metal will clog the injectors up. These are Piezo Injectors too, they're not cheap.

The reprogram is for after its replaced, I think you just need to get at that relay and see if it's the issue. Who knows what you may find back there.