Motion Jpeg is a lossy codec, but I really doubt that most viewers will see any difference.

I guess using a deinterlacing filter is not option, but the usually degrades when using it anyway.

I don't really know anything about SSD performance, so can't tell you whether a RAID array will be better or not. Your CPUs are very powerful, but can't tell you whether they can be a bottleneck here or not.

I recommend to contact Aver support and ask the doom9 community.