Given the fact that the 3000 series WX (pro) CPU's are around 3-5% slower in benchmarks than their 3000 non-pro counterparts, I reckon the 5000 pro series should be at the best 5-10% faster than the 3000 non-pro series.
I would recommend the WRX80 Sage mobo from Asus. I just built a 3000 series WX machine with it and it is a top-notch quality motherboard! I don't know about the MSI you could do some research and see what you need more of the options. The Sage has Dual Intel 10gbe ethernet which is a really nice feature. The motherboard also has a built-in Aspeed Graphics chip so you could run this machine as a rendering node without the graphics card which I am doing and actually save some money :).
Those motherboards support 2TB of ram so I guess you could technically populate all 8 slot with 256 but I am not sure. Check the QVL of the motherboard on what is supported.
Everything else seems in order apart from the cooler. I built the node in the same case you want to order (just without the window). The socket of the motherboard is rotated 90 degrees to horizontal. TR non pro cpu's on TRX40 motherboards have their sockets vertical. The cooler you mentioned in the text is not gonna provide a full coverage of the CPU and even if you go for a U14S TR4 cooler you will end up exhausting air to the PSU bracket which is positioned at the top of the case above the motherboard.
I suggest going for a waterloop or if you want to go with a fully budget option like I did then go for this:
Arctic Freezer 4U SP3
This cooler is rotated by 90 degrees, it provides full coverage of the CPU and will suck air from the 2 big 180mm fans of the Fractal torrent positioned frontally. Again since you are going for a windowed case this cooler is quiet ugly and I would rather go for the waterloop option!
Happy part hunting!