Complicated question I have. SSD,network,apps,boot-pool/speeds

If you selected two disks at install time for the boot-pool, they are mirrored.

Go to System, Boot, and click the Boot Pool Status button. A mirror boot pool will look like below image. You can also go to the System, Shell menu and then type in zpool status -v and hit enter to see the pools.

Your UGT-ST644R may be a problem also.
What’s all the noise about HBA’s, and why can’t I use a RAID controller?

Multiply your problems with SATA Port Multipliers and cheap SATA controllers