Maybe it’s clear this way:
For every 2 lanes you want allocated to the PCIe slot (up to 4), you lose two SATA lanes. Since there are 8 lanes total, but 12 possible lane destinations, they pre-made combinations of destinations that they think would be useful:
You could desolder it and solder a new one on, or possibly even solder one on top of the existing LED. Same as replacing any other on-board component.
IPMI generally only shares network access with on-board gigabit LAN, in addition to having its own dedicated IPMI LAN port. When you’re using high speed networking, generally you connect both the high speed (for normal use) and the dedicated IPMI LAN port (for IPMI).
You’re assuming wrongly, they use RJ-45 wall jacks even for telephone. The numbering suggests that D-1 is the only port wired for data, the T ports are wires for telephone. The punch down block at the top shows only 1 pair connected per destination —> telephone. To convert one of these to Ethernet, you’d need to pull it out of the punch down block and instead punch all 4 pairs into a CAT6 jack.
You’ll definitely need something with fast PCIe lanes for NVMe. Something with either PCIe 4.0 x4 coupled with a very fast SSD, or something with a lot of PCIe 3.0 lanes.
Is your RAM on the QVL? Ryzen’s notorious pickiness about RAM carries over to TR and EPYC, too. One of the first things before POST and BIOS splash display is memory training. If it can’t get past that, something about memory needs adjustment. Have you tried downclocking it?
Tried a different cable, just in case you’re capping out at 100Mbps?
Which protocol are you using to test file transfer? If it’s anything involving encryption, that CPU will be hurt real bad, with no AES-NE.
Number one cause of random hard crashes/hangs is RAM. Re-seat it, replace it, down-clock it, run a single stick, do everything you can to either rule it out as a problem, or to isolate the problem to a particular module or channel.