My first time building a gaming PC

Moin, after my trusty ready-to-use computer is now starting to wear thin with newer apps 8 years later, I decided to assemble the successor myself. I’ve already put together all the ingredients that I personally like the most. Here are the specifications:

CPU: Intel Core i5 10600K 6x 4.10GHz So.1200
GPU: 8GB MSI GeForce RTX 3060 Ti Gaming X LHR Aktiv PCIe 4.0 x16
SSD: 500 GB Samsung 970 Evo Plus M.2 2280 PCIe 3.0 x4 NVMe 1.3 3D-NAND TLC
Hard Drive: 2000 GB Seagate Barracuda Compute ST2000DM008 256 MB 3.5-inch (8.9 cm) SATA 6 Gb/s
RAM: 16 GB Crucial Ballistix schwarz DDR4-3600 DIMM CL16 Dual Kit
MBD: MSI Z490-A Pro, So.1200, ATX
PSU: 500 watts, be quiet! Pure Power 11 CM Modular 80+ Gold
CPUKühler: Be quiet! Pure Rock 2 Black
Status: Be calm! Pure Base 600 Good Midi Tower

My first issue would be the communication between the MBD and the GPU. My graphics card has PCI 4.0 as an interface, but only PCI 3.0 connections are identified on the motherboard at sites like Mindfactory.de and Geizhals.de. But that shouldn’t be a problem, the GPU will simply lose a fraction of its potential with an outdated connection. But now, the manufacturer MSI is advertising PCI 4.0 connections on the MBD, so who should I believe now?

My second question would be to connect the SSD, more precisely, where is the SSD connected to the MBD? I’ve never had an SSD before, only an HDD.

The third question is about available space, is there enough space for all components? The MBD and the PSU are not a problem, but I’m not sure about the GPU and CPU cooler.
Below are the dimensions:

Maximum graphics card length: 425 mm
Maximum CPU cooler height: 165mm
Maximum mains length: 210mm

CPU cooler: (without mounting material)
Length: 87 mm
Width: 121 mm
Height: 155 mm

The graphics card is 2.5 inches high and approximately 32.3 cm long.

Does this all fit, do I have to make changes again?
Thanks in advance for all the answers.