ASAP

Its not done until NAV RDY is flashing. It takes 4 minutes. You'll get the solid NAV RDY around the 2 minute mark. If you've done it right the top right of the CDU will say D5/B1 once you switch over to NAV.

Pressing enter on the HUD takes a "delta" which is the difference between your GPS derived altitude and the altitude derived from your altimeter. In the sim it's not really simulated, but when you hit enter the number that your jet is deriving for the delta pops up. It's showing a zero for Delta and GPS because in sim land there is no difference. you hit enter again to accept the values. If you hit enter and you saw XXXXD over XXXXG it would mean your system is messed up and you need to manually enter a delta value through the IFFCC menu. You'd basically ask your wing man what delta they got and copy them, or you'd reference the weather planning data you took off with.
Without getting too far into the weeds, when you do that you are storing those numbers in IFFCC. They don't really matter until you have an issue with your GPS or jamming that degrades your FOM to something worse than D5/B1 which indicates you didn't have a good GPS altitude source, you'd set that little switch "alt source" switch on the AACP (middle row on the left, it normally is in "baro") to "delta" and it'd use those values to calculate your actual altitude vs the altimeter altitude. 

That's all really important for the bombing triangle and your jet being able to accurately calculate weapons delivery stuff...  but again, not really important in a virtual environment that is far simpler than real life.

I take it you live in a city... I've flown my own airplane at night a lot. I assure you the inky blackness is realistic on a moonless night. Even with NVGs picking out individual targets would be next to impossible. Using the TGP and strafing the diamond/IR marker is the actual solution that A-10 pilots use for this problem.
 
You can go into the IFFCC menu and change the settings so the pipper does not occlude the TGP diamond. Also use the IR marker from the TGP.
 
Also not all that unrealistic. your TGP shouldn't gimble unwind if you're attacking between 25-50 degrees of strafe. That might help. Also, lase the target and take a mark, make the mark SPI or a Steerpoint and slave the pod to it. that should keep it fairly close to the target.
Or have a buddy lase/IR mark the target and strafe the LST or his IR marker.

The results you talked about sound reasonable and accurate. There's a lot to breakdown here:
Perfect. Put your SPI at the base of the target, missing short is generally better than missing long because bomb impact angles and fragmentation patterns.
 
 
CCRP is very accurate even from much higher up. The ballistics of a conical fin MK-82 are very well understood and the computer does an excellent job of putting a dumb bomb right where you want it. The limiting factor in a level CCRP delivery is YOU being able to get the pipper right on the ASL. Of course, the winds blow. The jet has its own wind table that you shouldn't (but can) mess with. Its possible they will push the bomb off the target especially if there is elevated terrain making the wind whip around and unusual velocities and angles through the bombs flight path, but in general the jet does a great job of calculating winds into the release parameters.
IRL there is a minimum guide time for the GBU-12 to be able to hit its target which drives a minimum altitude you can release the bomb. Also the lower you get the more you have to deal with things like podium effect. If you drop the bomb in one spot and then fly over the target, 15 seconds later the laser might be pointed at the back side of the target where the bomb can't see the laser spot. The issue is not as pronounced up high as it is down low.
Just like with your SPI, pickle at the base of the target. Factor in your reaction time between when you think "Time to pickle" and when the button is actually depressed. If you continually miss long, pickle shorter of the target. CCIP diving deliveries require some skill and know how to do correctly. Unfortunately there isn't anything official teaching you how to do that in DCS. There are some good videos out there that attempt to explain it. IRL any diving delivery is flown with specific parameters. Its not as simple as tipping in and killing something. You would do a specific delivery like a 30 degree dive bomb or a 45 degree high altitude dive bomb for instance. Those each have a very specific base altitude and offset, and then you roll in and point at a specific aim off distance from the target, and set the target at a "Initial Target Placement" in the HUD. You'd also set your desired release cue over the target, which is based on your desired time of fall which is also set by the delivery you are trying to do. All that is to say that CCIP deliveries are complicated and need to be practiced and you don't have the required data you need to do it correctly, so missing isn't surprising, and I wouldn't stress too much about it.
CCRP is way more accurate than your average DCS user doing diving dumb bomb deliveries because CCIP is difficult to do correctly. As far as laser guided bomb accuracy, there are some nuances that might be causing issues trying to use them down low. Without seeing you actually use them I can't speak to why they are less accurate. The GBU-12 if unguided or not guided properly is draggy and I would expect it to fall short.

That's just because of wind. If it is bad enough that it is impacting your ability to employ weapons then you need to change up your run in heading to be more into or out of the wind. Otherwise for navigation, line up the arrow at the bottom of the hading tape with the captains bar for a wind corrected heading to your next waypoint.

Of all the systems on the jet this one has the lowest fidelity of how it's actually modeled. None of the CMSP or CMSC is actually accurately simulated, and there are a ton of differences between the real system and the way it's modeled in DCS.

Hugely depends on the mission and the AO.
but super generic...
Front - Strike freq for talking to your JTAC
Mid - interflight to talk to your wingman
Aft - Air coord freq or "common" with other air players, or for monitoring the AWACS/CRC.
 
Other options...
Front - Strike
Mid - Air Coord, AWACS/CRC
AFT - Interflight
Typically you'd use the front radio to talk to ground/tower/departure/approach as well. You'd do the majority of your jumping around between frequencies on the front radio. You'd pretty much leave your inteflight set the whole time, and the aft radio you swap as needed.

That is incorrect. The NVGs sit about 1/2-3/4 of an inch in front of the eyes. Pilots have to look under the NVG tubes to see anything inside the cockpit. It's like flying with bifocals. The NVGs are only good for seeing outside the jet. Everything inside the jet is an unreadable blur. The NVGS cannot be closer to the eye than the HMCS monocle, assuming you are using HMCS.
Granted, that's not the way DCS represents it, and you can't really simulate looking beneath the NVGS to look inside. On the NVGS everything is unrealistically in focus in the game.

You can only edit the 50 waypoints in the mission database. The remaining 2700+ waypoints are loaded into the system but you cannot manipulate them. I haven't encountered the ?-1 before, but if I had to guess I'd say that it would overwrite waypoint 1 in a similar fashion to how your markpoints will cycle from Mark Y back to Mark A.

are you expecting the old circle pipper looking thing in the center of the HUD? That’s not a thing anymore. 
Are you getting the LAR and staple on the left of the HUD? 

That is normal and accurate.  It’s just the analog guage and the digital system not being perfectly synced. The analog guage isn’t super precise. 

That’s normal. It’s a function of head position in relation to the hud glass and the projector. Pilots have to move their heads slightly to see stuff at the far periphery. In flight the horizon line should be visible due to the AOA of he jet. On the ground it’s normal to not see it without leaning forward/down

Pro tip from a real a-10 pilot. Just don’t use auto lase

Basically if the > on the left of the screen is inside the bracket immediately to its right the bomb will make it to the target. If it’s pointing at the bottom part of the bracket that has a bar the bomb will hit the target at the desired impact angle set in the profile page. The vertical steering line should be lined up in the center of the HUD frame (put your GBL on it) for best bomb range. The verticals line is a steering reference only though. As long as you are in LAR the bomb can get to the target. 

F1433 I’m 
pretty sure means the E-3 you have hooked has 143,000 lbs of fuel remaining
the G2A4B+R is the weapons load out that it is reporting over the link. 
I rarely look at it so I’m a little fuzzy on what the letters mean. I think it’s something like Gun, 2 A/A missiles, 4 bombs, rockets. But I could be wrong about what exactly they break out to.

Not it shouldn’t if you set QTY 3 you’ll get three bombs. System is working correctly. If you want 6 bombs select rip pairs / QTY 6
the quantity is the quantity of bombs not the quantity of pairs of bombs. RIP pairs just means it will release two at a time, wait a few milliseconds and then release a another pair, wait, release, etc…
In your case it performed correctly. it dropped the first two at the same time, one from each TER, and the third a few milliseconds later.  When bombs fall off TERs they alternate between symmetrical TERS (not stations 5/7).
 
So if TERs are on 4/8 and you rip pairs you’d get the center bombs from both TERS. Then the next pair you’d get the left bombs, and finally the right bombs.  If you dropped rip single you’d get 4 center, 8 center, 4, left, 8 left, 4 right, 8 right. 

For the same reason you don’t have one switch that turns on every piece of electronics in your house all at once. You want to be able to manually decide what you want to turn on and off. Also if something breaks you want to be able to isolate it and turn it off without causing problems. The kind of automation you are talking about comes with a lot of interconnection that makes things more complicated, costly, and more difficult to troubleshoot.
Also it makes maintenance on the jet a lot easier which means it can be done faster which means the jets can fly more missions which means they can kill more stuff. That is very important in war. More modern doesn’t always mean more complex and automated.

The maverick is always showing WHOT. The boat switch and the crosshairs are telling the missile if it’s looking for a hot object in a cold back ground (white crosshairs) or a cold object on a hot background (dark crosshairs)

a picture is worth a thousand words... The simple answer to the original question is that the elevation of your current waypoint (Which is refered to a "Steerpoint") is on the steer info page next to EL (see the red box below). Here it says 33 because Steerpoint 1 is at 33 feet MSL (probably at Batumi). Get to steer info page by pressing Function 0 on the UFC or by rotating the rotary switch to Steer

I always use latch on and never use the auto laser function. I want direct control over when it turns on and off but I don’t want to hold the button down forever if I’m lasing something from high altitude or if I’m moving the jet. 
 
downside is DCS has a silly notion that the laser burns itself out and becomes inoperative after even a short time of continuous lasing and so you have to be disciplined about turning your laser off. 

From my understanding it’s not an often used feature. They just select EO power on when they FENCE in. Most pilots I’ve talked to said they much rather make positive switch changes rather than relying on a system to do it passively, because that way they know for sure it is done. Or alternatively they leave EO power off until they start thinking they might want to use it (i.e they get passed a line 5 of “Armor”). I believe for the health of the seeker they don’t like to leave them running unnecessarily all mission.
 
As far as which one you use t’s an either or. pilots can either choose the system to auto select EO power on when I cross a certain steerpoint, or I can tell it to turn on 10 minutes after my scheduled takeoff (for instance). I can’t tell my jet to turn it on 10 minutes after takeoff and turn it on at a certain steerpoint because those are mutually exclusive commands. 
 
To your actual question though, I suspect in the real jet though if you input a time it would override the steerpoint option and the other way around. Cant speak to how the real jet handles that but it would be consistent with the general way the systems seem to work. 

The changes were made to reflect how the jet should be when the pilot arrives at the jet to accept it from maintenance.

As the pedals move forward and backward when you use the adjustment handle (opposite the alternate gear extension handle) an arrow moves up and down that scale to tell you the position of the pedals. It’s just so the pilot can quickly set them to the same spot every time in every jet they fly for consistency sake. It’s important for muscle memory and repeatable habit patterns I guess

I am not at my computer to test it but I thought if you go to the waypoint page and re enter the MGRS coordinates it forces the system to pull an elevation from its terrain database and overwrites any manually entered elevation. 

What was your altitude? even at 15 degrees of dive depending on altitude it might not be able to compute. for the A-10, unless you are down low (<1000AGL) 15 degrees is a really shallow dive angle it could be the aircraft was unable to do its look-aside ranging properly if you were too high/shallow. Try pointing the nose 30-45 degrees nose low and you'll probably get a CCIP solution. If that doesn't work then I'd need to see a video or something to figure out what you're doing. CCIP doesn't care about your SPI, you should get accurate symbology even if your SPI is on the other side of the planet.
One other thought: were you in GUNS mode in the HUD vs CCIP with some other weapon profile called up? Its possible have the gun pipper in the HUD while you have CCIP rockets or bombs selected at the same time. It could be the CCIP INVALID was for the rocket solution or something... I'm just spitballing ideas what could cause it really.
Like I said, try getting lower/steeper with your guns passes and see if that helps. If it doesn't work then maybe theres some other switch error somewhere with EAC or LASTE.