I would go full custom loop, but that’s just me…
Either way you will have a hard time finding a case to pack all this into and keep it cool. Water-cooling 2x3090’s means you want at least 2x 240mm radiators. Water-cool the CPU too and that’s another 240mm radiator.
FYI: the 3960x, 3970x, 3990x all only have 64 lanes.
8x to chipset
32x to your 2 3090’s
leaves a max of 6 m.2’s direct to CPU (if the motherboard doesn’t use some lanes for things like 10gb nics or usb).
Any remaining m.2’s would run through the chipset (and take a performance hit)
You may find you don’t need the full x16 lane for you workload. Things like mining can run fine on x1 links (for example), but you would probably have to test this to be sure.
The Threadripper pro CPUs that are coming out will have more lanes and the motherboards will probably reflect it with more connections (M.2 or PCIe slots) at the expense of cpu clock speed.
If you don’t want to watercool:
Gigabyte Aorus Xtreme or ASUS Zenith II Extreme Alpha
2x AIO type 3090 in slots 1 and 3, mount radiators in the case somewhere
2x AIC’s with 2 M.2 SSDs each (probably have to buy the 4x m.2 models and only fill with 2 SSDs each.
OR
2x PM1735’s or something similar. Higher capacity, higher cost, but enterprise grade.
run 4x m.2’s on the motherboard
On the Aorus Xtreme it would be 2x to CPU and 2x through chipset
The Zenith II it would be 1x to CPU and 3x through chipset, it uses 4x lanes for USB-C according to anandtech
That would give you 29.6TB of SSD if you used the 12.8TB PM1735’s and 1TB 980 Pros.
Not to through even more decisions into the pot, but…
You could get some M.2 to SFF-8643 adapters and then run some higher capacity U.2 drives like the PM1733 and then each one of the M.2 slots would give you up to 15.36TB bringing the total up to ~87TB of SSD.
More yet, you could run 2x U.2’s on each of the x8 PCIe slots (not sure about the right adapter here) and then get up to ~122.9TB of SSD at Gen4 NVMe speeds.
The enterprise SSDs are costly though…
If storage (space and speed) and GPU is more important for your workload than CPU clock speed you may look at an EPYC based or Threadripper PRO based system. Both support 128 lanes of PCIe Gen4.