How is your memory load? My guess is you've reached the part where your SSD-speed (both reads and writes) is the limiting factor due to the low RAM. There's a huge difference between SSDs: some have very bad performance when it comes to combined reads and writes. If it's a budget SSD, that may be the cause.
total used free shared buff/cache available
Mem: 7909288 1471828 127476 235508 6309984 5935240
Swap: 2097148 1010240 1086908
I have not used #free before but the numbers don't seem to look to bad and are similar to your outputs. Still not explaining my slow times as far as I can tell.
Also after updating the dbcache setting still ridiculously slow like .09% per hour. Like 10 times too slow.