Building a FreeNAS server

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After motherboard failure and problems transferring the RAID 1 setup I decided to try the software RAID in Windows instead. It was horrendous and was taking 5 hours to get to 17% for 2x1TB partitions that are half full. They just sat then endlessly grinding away.

I've decided it might be best to build a FreeNAS server instead. I don't have any experience with using a NAS and would appreciate any helpful tips. I have a spare case, PSU and a D1800B-ITX board but it only has 2 x SATA connectors. I want to put my current 2TB drives in there so that's both the slots used up. I assuming FreeNAS needs it's own drive to run from? Could it be ran from a USB flash drive? Because I want the 2 drives to be in a RAID 1 I don't know if it could be installed onto that or not. The board has a PCI-E 1x slot so I can get a SATA controller if it will be problematic.
 
You used partitions for RAID1 rather than use separate drives? Either your terminology sucks or you missed the point of RAID.

The FreeNAS forums have a wealth of discussion on hardware specs and suitability. A 2 port board and a 1x PCIe slot combined with a low end CPU don’t fill me with happy thoughts personally - it’ll work, but it’s very limited in terms of expansion options going forward.
 
I used software raid0 in w7 and it was faultless. Maybe used it for about 6 years ..many pluses and no real minuses except not being able to boot from it. easilt transferred and imported on another win machine, no appreciable overhead, good speed up...on reads and writes.
Freenas has many fans but is rumored to require lots of memory.
Your problems sound like you may have a dead or dying disk ..1000's of disk errors will slow any copy down especially when it retry each error up to 10x times.
scan your disks using diskcheck full surface scan.
you may be better off running xpenology v good and v liteweight boots from a usb stick. Stick to dsm5.2 initially
 
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