Feedback on a dual RTX 4090 build.

Few things to touch upon here. The dual RTX 4090's for the larger LLMs should work fine. Gaming wise, you'll mostly only be using a single GPU unless you use an API that supports explicit multiadapter mode (DX12) or Linked Display Adapter (LDA) mode through WDDM. BG3 might be able to do this on Vulcan, but BG3 on Vulcan also has some crashing issues at the moment, so I'd still recommend DX11 for stability.

On the hardware selection itself;

• The CPU and motherboard choice looks fine. The 13900K is a solid option no matter how you slice it. If you want longer platform longevity, you might consider looking at AM5, but AM5 memory support is wonky when running 2DPC and multi-rank kits.
• Your memory selection is worrisome. 2x48GB at 6400Mhz is going to be hard to run on most processor memory controllers without some manual tweaking. Getting 4 DIMMs to do this in a 2DPC configuration on just XMP alone is going to be nearly impossible. This means you'll likely need to do some manual voltage/timing adjustments to make 6400 work, and even then, there is no guarantee. MSI is listing 2DPC dual-rank DIMMs at 5600Mhz max: https://www.msi.com/Motherboard/MPG-Z790-CARBON-WIFI/Specification

• The two RTX 4090's you plan to use won't do well in the Lian Li Lancool II chassis you selected. Both GPUs have a 240mm AIO and the chassis doesn't really support 240mm AIOs in a way that is conducive to having them on a GPU. If you are looking for single/dual slot 4090's in a multi-GPU configuration, you'll likely need to use a water block and go with a custom loop. I get that this is your first GPU build and that custom loops would be very daunting for a first time, I'd still recommend this route since you can add a CPU block to the loop and cool everything with a couple 360mm radiators. We offer build services to help if you would rather us perform the labor. For your specific workloads, I would actually recommend soft tubing and quick-disconnects. This makes servicing the loop and swapping in new components a very easy process without having to drain the system.
• I'd definitely recommend sticking with the 1600W PSU if you are going dual RTX 4090's. It'll be easier on the PSU in the long run and should put you right in the best efficiency curve of the PSU when under load.

If you want to avoid custom water loops, I would probably go with this chassis instead: https://www.microcenter.com/product/660146/lian-li-v3000-plus-tempered-glass-eatx-full-tower-computer-case-black. It's extremely pricey, but it supports an inverted motherboard tray and has plenty of space for you to mount both radiators from the GPUs without the NH-D15 being in the way of your tubing. You can see the different configurations on Lian Li's website: https://lian-li.com/product/v3000-plus/.

Definitely looks like an interesting build though, wish you the best of luck with it.

If you are going the route of a custom loop, we can definitely make the Lancool II work. In fact, I'll give you a picture of a new test bench I just built in our lab for GPU testing:

This loop is designed for us to use quick disconnect fittings to add/remove hardware quickly so we can test both waterblocked and aircooled cards with minimum downtime.

Now to answer your questions;

1. A single 360mm radiator + 240mm radiator might not be enough to cool both RTX 4090s unless you are comfortable undervolting them. Adding the CPU to the loop is also going to add more heat as well (roughly 300-320W under load) and unfortunately that extra 120mm radiator won't really help much there. I would either air cool the CPU and run both GPUs in a loop for this chassis, or run a single GPU in the loop and air cool the other card. Since the blocked card is single slot, you might be able to do this without an issue.
2. 5600Mhz would be far more doable. It might still require some slight tweaking, but it should be doable. I specialize in memory overclocking so this is something I can help you with here on the forum.

As for the loop designs provided, I like your QDC placements, they should work fine. One issue I overlooked was the PCIe configuration of your motherboard. The bottom PCIe x16 slot is only wired for PCIe 4.0, and only x4, not x16. This might present a bottleneck in PCIe bandwidth as the slot is also wired to the board chipset and not the processir:

I can't find any details online as to whether or not the top PCIe slot supports PCIe lane bifurcation to split it into two x8 slots. This might be a challenge if you already have this board and are planning to get the most performance out of the dual 4090 configuration.

Some additional advice on the watercooling side of things. I would probably recommend foregoing the rear 120mm radiator. QDC fittings are already going to restrict the flow rate quite a bit. This coupled with using multiple water blocks will result in loss in head pressure. Both the modern DDC and D5 pumps offer a solid flow rate, but head pressure is often difficult to maintain. Instead, you could use a 120mm DDC pump like the one in my picture above, or use a 240mm D5 pump mounted above the PSU shroud.

Also, I know conventional wisdom states that slight positive pressure is better for a system, make sure every radiator in the loop is configured to exhaust. You do not want to dump hot intake air into the chassis, only for the second rad to pull that hot air in. Both being set to exhaust will result in better thermals, but at the cost of dust buildup in un-filtered areas of the chassis. Keep an ESD safe duster handy to clean every month or so.

Lastly, it might be worth considering using an external radiator since you are going with QDCs. You can run a 360mm + 240mm for gaming, then connect your loop to an external radiator for when you are running intense high precision operations on the GPUs. You can cut some holes on the back of the chassis add circular rubber grommets and run soft tubing out with a valve on them so you can swap seamlessly. I loved my old MORA3 radiator and it by itself could cool both your GPUs and CPU with relative ease. The thing was massive: https://www.performance-pcs.com/water-cooling/radiators/watercool-mo-ra3-420-pro-black-wc-25120.html

When done right, it can also look amazing too: https://www.youtube.com/watch?app=desktop&v=QXv1owX8zx4