Copacetic

Looks like a Deepcool Matrexx 55 (v3 specifically) with some extra RGB fans. A 4000D Airflow would be a much better choice.

Fractal Design Meshify 2 Compact with the solid side panel? Same internal layout but without the sound damping foam, and of course the more open front panel. https://www.fractal-design.com/products/cases/meshify/meshify-2-compact/Black/

If you buy another Noctua cooler for the Xeon (socket 1150?), then yes the mounting hardware you already have on the motherboard will be reusable.

This SSD tier list puts them in a similar rank, while this one puts the A2000 as the slightly higher performing drive. The main difference (other than slightly different read and write speeds) is that the SN550 lacks DRAM. Both have a 5 year warranty so you should probably just go with the cheaper one. If you were splitting hairs, the A2000 will probably give you better performance, but both will be good enough.

Assuming that it is a regular NH-D15 and you have proof of purchase you should be able to contact Noctua and get the AM4 mounting hardware (NM-AM4) Follow the information on this page or simply buy the kit from a retailer. If you were to buy another Noctua cooler with the SecuFirm2 mounting hardware you should in theory be able to reuse the mounting hardware that is already installed (and a new Noctua cooler would probably come with the AM4 mounting hardware).

The GPU temperatures are already pretty good in this case. This review has some great charts showing the temperature change by just opening the door. You can probably drop the CPU temperatures further by installing the vented top panel that came with the case. The GPU temperatures did not drop much at all, but the CPU gets a 10C decrease. The only downside is that the noise levels increase.

It seems like you have a slightly negative pressure. While there are the same number of intake fans as exhaust, the intake on that case is restricted in comparison to the exhaust fans. Perhaps try and increase the intake fan RPM / decrease the exhaust fan RPM?

According to this tier list, it is not quite enough for a fully maxed out 3900X with little airflow. This Gamers Nexus video talks about it, saying that it is more than capable of handling a 3900X at stock speeds. Should be fine so long as you give it some decent airflow over the VRM.

The vibrations might be from the bearing type (rifle). In this (albeit old) article it says that I believe that sleeve and rifle bearings are similar, so the fans you have are probably best mounted vertically. You should try mounting the currently horizontal fans vertically to see if it is the mounting position that causes the vibrations.

Unless you need the X570 chipset there are B550 motherboards coming soon with some decent looking mATX options

The thermals of the 500DX are quite good. Adding and extra case fan does not help the thermals for either CPU or GPU. If you wanted to you could move the top exhaust fan to front intake.

Here is the review by Gamers Nexus Overall the thermals are not horrible, but getting the airflow panned would improve the airflow.

Phanteks says it can fit a PSU up to 270mm (including cable)

Well you would expect the next card in the Titan series to be better than the previous one...