Not sure if I fully understand the question you're asking, but here's my take:
A lot of discussion is made about the D2's being unreliable because electricery, but so far I've found it to be anything but the case. To start with, I've done countless water crossings such as in my avatar, and some number much deeper than that, with no problems, and no preparation at all. While it is true there are more electronics on the vehicle, it's also true that the electrical technology, and in particular the connectors, are more reliable than before. From what I've gathered, carry a spare crank position sensor and know how to change it. Go through your truck and put dielectric grease in all the connectors. Yes, the SLABS unit could fail (three amigos) but this leaves you no worse off than if you didn't have it in the first place.
The only lingering terror I have is getting stuck in water over the floor pan, which will come in, and the body control computer is under the driver's seat. Something needs to be done about this. There are 3 more computers behind the passenger kick panel, which are a little better off, but something needs to be done there too.
I recently witnessed JK Rubicon get stuck in water which was over the glove box lid for 2 hours. After recovering him, the truck drove out under it's own power, but did suffer damage to the passenger airbag module, electric cooling fan, alternator and a cell phone. Not too bad in the grand scheme of things.
I've found the venting on the headlights to be a problem. There are 3 vents for 1 chamber, which allows the water to siphon in. I plan on running breather lines, or at the least plugging two out of the three vents on each light. Just one minor detail. The breathers for all the fluids also need to be extended.
I've swapped in an Odyssey PC2150 battery as a simple major upgrade to the stock system. It's easy, completely uncomplicated technically, and increases the electrical reliability greatly. However, with a single battery system you do still run the risk of having a dead battery. I will likely work in a small backup battery, something like a PC680 which I have proven is more than capable of starting and running the truck, and is easier to install somewhere than a large battery, with a simple manual transfer switch.
The CV joints on the front driveshaft get a lot of criticism. It's true they are prone to failure without warning with disastrous results. Either change them out for greasable units, or change them pre-emptively with a new set of non-servicable units and ignore them for another 60k miles.
I went with 245/75/16 Cooper Discoverer ST/C tires, which I'm happy with. They don't look super aggressive, but they seem to get the job done. They wear like iron, the ride is OK at 40psi, and work acceptably on snow and ice. I even used them up north when I was a recovery crew at Rallye Perce Neige, which saw me driving *with pace* on ice and snow for 16 hours where they performed well. I don't think this could be accomplished with swampers. They're good on the highway, I don't need to regear, they balance well...
And I went with HD OME springs and shocks. I think the 2" lift really improves the capability over stock, without getting too high that CG is a huge concern. I believe they're also stiffer than something like the RTE springs which helps stability and load capacity. It really just depends on what you want to do with the truck.
Overall, my truck isn't too high. I can still fit in my 7' garage door, WITH a light bar on the roof. It's relaxed to drive on the highway, and as I mentioned above, performs surprisingly well trying to keep up with a rally on twisty mountain roads.
One thing I don't have yet but I think is critical is swaybar disconnects. I don't like driving on-road with the swaybar removed, but the difference off-road is so incredible, and you really need the flexibility when you've got small tires and stiffer springs. Swaybar disconnects just make the situation so much better. The only drawback I see is the potential for more transmitted noise due to the links they're using? But I don't know yet.
The front bumper is another contentious issue. I went with the ARB, and was pleasantly surprised that the mounting system for the 04's is different than the earlier models. I think it will be much more resistant to tweaking. It does suffer on approach angle, but I really haven't found it to hold me up on any trail that the rest of the truck was capable of anyway. I also wanted more protection for the front of the truck compared to the razor blade bumpers. Access to the winch isn't the greatest, but hasn't been a problem yet.
I haven't yet but will get a steel rear bumper because it's pretty much impossible to not drag your MMM over everything. I've already ripped my plastic one off once.
The braking system is pretty good as-is, I recommend sticking with standard rotors and I like the Ferodo pads I recently swapped to. I think some of the other blingy setups are just wasted money. I could make the same glowing remarks about their performance as you read about the blingy stuff, but the reality is that any time you put new brakes on an old truck, they will feel wonderful compared to what came off.
It really depends on what your goals are with the truck. I found this setup to GREATLY increase the capability of the truck, while having almost NO impact on the long distance driveability or reliability. I have yet to encounter a trail that it wasn't capable of with the following caveats: There are some obstacles I've taken bypasses. There are some obstacles which maybe I could have done with more clearance, but would really have rathered be on a winch line anyway. I find that once you start building up bigger than this, you start driving past these trails, looking for trouble. If you build up bigger, you start losing on-road capability, and then have to look for harder trails to challenge the truck... and if that's your goal, there are so many other platforms that are a better starting point than a D2 anyway.
So far I've been happy with my approach to keep it lower and smaller, but then armor the bottom to take the inevitable hits. I've got the QT diff guards, which are lighter duty than the sewer cap mod, but I like that they act more like sliders than a battering ram. I also REALLY did not like the idea of welding on that sewer cap because I would think there's going to be a lot of warpage on the axle, unless it's only tacked on but... the details of it weren't clear to me.
Now this makes driving on trails much less nerve racking because I'm not constantly worried about tearing open the diffs. The next most vulnerable thing I've found is the track bar which I keep bending and have to do something about. Beyond that I've got an idea for an integrated mid-section skidplate frame combined with rock sliders. It would be a large frame to support skid plates, and would be stronger than typical rock sliders so that I could build in nerf bars without worrying about them tweaking up.
But, that's in the future. As I say, my goal is to keep it low, uparmor the bottom, keep it streetable, and just decide what you want to do with the truck.