GPU - I'd recommend against the Ventus model if you care about noise. The MSI Ventus (and Shadow) are generally significantly louder than basically any other option. I personally have the PNY model and find it extremely quiet.

CPU - The 9900X isn't faster than the much less expensive 9600X in the vast majority of games, only very slightly faster in the few that it is faster, is just as often slightly slower, and always slower than the 9700X. The Ryzen 9 CPUs are dual CCD CPUs which are essentially two Ryzen 5 or Ryzen 7 CPUs glued together. For non-gaming applications that make use of a lot of cores, these can offer significant advantages. But for gaming they're almost always slower. This is because even though they have higher listed clock speeds than the less expensive CPUs, those higher clock speeds are only ever seen when only one core is active. Otherwise the mere existence of the second CCD means the CPU ends up running a lot hotter and boost speeds drop faster thus that once you get to 4+ cores being used they generally even out with the lower end CPUs in clock speeds and may even end up slightly slower by 6-8 cores. Most modern games are generally single thread limited, so single core performance is important, but they and the rest of the operating system and background applications are going to be spreading themselves out over several more threads making those peak single core clock speeds mostly a "fun fact" with little real world benefit. The 7800X3D is also similarly priced to the 9900X and is around 20% faster in games.

Motherboard - I would recommend against the MSI B850-S for a 9900X, and even for a 9600X. For the 9900X it may struggle to deliver it full power if you do ever make use of all of that CPU's cores. But the main issue I have with that motherboard is that it only has two M.2 slots. M.2 slots are going to be what you're going to want to use for all storage, and only two lots greatly limits future upgradeability. I'd recommend at least the B850-S EVO if you go with the 9600X, but more the Gigabyte Eagle AX (B650 or B850 model) as it's less expensive than the MSI B850-S EVO and higher quality overall.

PSU - I would probably recommend the NZXT C850 Gold Core instead of the Corsair RM1000e. The RM1000e is a perfectly good PSU, but the NZXT C850 Gold Core is extremely efficient and quiet with the same warranty length for less. You also do not need 1000W here. 1000W is what you need if you go with a 9950X and RTX 5090.

Case - Consider the Lancool 217. A bit quieter, a bit cheaper. And assuming you don't care about ARGB fans, it has none.