Flickering headlights and flickering blue high beam indicator on dash?

Hey there Bruce, I will grab those diagrams for you right now. The Daytime running lamp system has its own control module. Have you taken a voltage reading right at the Alternator stud? Since the head lamps are a high current draw, see if you have good charging system voltage with the head lamps on, that will load the electrical system. I would see what youre getting for voltage right at the headlamp connector as well.
I will get the wiring diagrams ready for, but checking for voltage drop when the circuit is loaded with the headlamps on, both on the positive and negative side to see if there are any connection issues on either leg. Pretty strange on the Monti Carlo.

Diagrams 1, 2 are for the Sealed Beam headlamp bulb, diagrams 3, 4 are a composite type. The circuits are pretty much the same except with the exception of the composite type uses a ground for each side headlamp, whereas the Sealed Beam shares a ground from one bulb.
I clean grounds even if they look ok. If theres any paint under a grounding location or corrosion, I make sure theres a solid ground since they are overlooked quite a bit.
Since the wires are all Black for the headlamp grounds, with the headlamps On, measure the voltage from the Black wire(s) to Battery Negative, do the same on the power side to Battery Positive. You should have a very low reading, towards 0volts.
You can do the same measurements from the engine block and body/frame to Battery Negative as well, checking for the same loss of voltage.
Its pretty simple setup, but do check the charging system, make sure it can handle the extra electrical load.

Correct. One setup shares a Ground and the other has a ground per side.
Does the flickering stop with the DRL fuse in? If it stops with the fuse in, I would leave it in. Daytime running lamps are standard on modern vehicles anyway and is not going to hurt anything.

If you want to continue testing and attempt to figure out whats causing it, see what dc voltage reading you get while the truck is running with the head lamps on High with the Red meter lead on one of the head lamp ground wires and the Black meter lead on Battery Negative. That will give you the voltage drop (or loss of voltage) on the ground side, between that head lamp connector and battery Negative. You dont want to have any voltage loss, but since you will have some, it should be a very low reading. Do this test on the power feed wire to the headlamp connector and B+ as well.

I understand this type of testing can be confusing sometimes because its the more advanced method than just reading the resistance of a wire. Resistance readings on long stretches of wire is almost pointless because the circuit is not loaded. Things change when there is a lot of current flowing. But do that test above, dont do multiple tests without knowing what the first tests results reveal. The flickering might be an issue with the route current is now taking because of that fuse being out though. Something to consider.

How about leaving the fuse in and just pulling the DRL Relay? Id be curious just to see how the circuit reacts, it looks like that should still work, while still providing power to the control module. Thats something you'll just have to try.
I did see some troubleshooting section too, here for the Daytime running lights staying On. Im not sure the point of this test is though.

The sealed beam is the older style, where the entire headlamp was replaced. If you remember kind of back in day when it wasnt just a small bulb change (composite), it was that hole headlamp that plugged into the harness. You voltage readings sound really good actually. Ign.1 Im assuming thats is a data PID on your scan tool, its a measurement the ECM is taking on one of its battery power inputs. A computer this old is not going to be too sophisticated.
You could also check for any AC voltage at the Alternator post to Batt negative. I use a scope when checking but a meter will work. Set the meter on AC voltage, turn on a bunch of electrical loads again and you really want to see less than 100mv on, so set the meter on a low setting.
If the flickering issue is gone for now, and you really want the DRL off, see if the relay removed acts the same way.

Yeah, they look great, super bright. Grounds get neglected so much because people dont think about the return path for current. But Im glad you took the time to do the extra work with the battery and tray. It all ends up back at the battery. I am in NC. We just got slammed with over a foot of snow. The worst part is they just are not prepared here with trucks and salt. Im from up north, so I can drive fine in the snow, but this place shuts down when it snows an inch.
Im looking through the power distribution diagrams right now to check on any battery saver type relays or fuses.

That loaded battery voltage being 12.9 is kind of borderline, but temperatures are just ridiculous right now.
There is a power module that is reserve power (36volts) for the airbag (SRS) system and power for diagnostics. Airbags are something you probably dont want to mess with. Setting off the airbags by accident can be extremely dangerous. Manufacturers usually have a flow chart for how to check certain sections of the SRS circuits.
What was your plan with the headlights now that they are working ok? Do the headlamps work ok with that fuse out?

Well since the Alternator puts out AC voltage it needs to be converted into DC voltage, so there is a diode trio. The diodes only allow the DC element through, when the diodes start to fail, and its usually just one at a time, there will be AC voltage spikes whenever that winding of the alternator comes around and it sends out the voltage. Its something we would use a scope to observe. But you can just do a search for "bad alternator diode waveform" and you'll see a picture of where there is a negative voltage spike.
The low voltage is a little concerning, that alternator was struggling awhile with bad grounds and a weak battery. Heres a guide on alternator testing. Where are you located ?

https://www.2carpros.com/articles/how-to-check-a-car-alternator

You can purchase access to service info for a number of days per vehicle if I remember correctly. All Data and Pro-demand I think both do that.

Hey there Bruce. I would be a bit concerned first with getting a good battery terminal connections, both on the positive and negative side. If youre having trouble getting a reading with a meter on a battery terminal, such as these sometimes painted terminals. Its going to be a little difficult to get a accurate reading if there is some connections that are not as solid as they could be. Theres some different specs when it comes to AC voltage ripple, 50-70ma is what Id like to see, but nothing is perfect and different vehicle makes have different max voltage readings.
But when a diode fails you will get AC voltage spikes and readings. Check your meter leads as well. Just connect them together, set the meter to Ohms and shake the leads, the resistance should stay a solid 0 Ohms. Meter leads that are starting to wear can really throw you down a rabbit hole, giving misleading readings.
When a diode fails, the alternator needs to be replaced or rebuilt, some places still do that.

https://www.2carpros.com/articles/how-to-check-wiring

https://www.2carpros.com/articles/how-to-check-a-car-alternator