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Update 1

I've written a script to go through the database and call OPTIMIZE TABLE on every table. I do not think that was done before, ever... After I've done that, pool usage value jumped to %95+ on all servers but the efficiency value decreased.

I am not a dedicated mysql admin but my friend and I have been working hard to fix the badly configured mysql files. We have reduced our number of pools to 2 from 20 and increased pool size to 90GB for a 124GB ram server. I've also enabled file_per_table. What is bugging me is the constant spikes in disk read/write speeds. Picture below is while the server is under decent load and it has been up with the updated config for about two days.

I am not a dedicated mysql admin but my friend and I have been working hard to fix the badly configured mysql files. We have reduced our number of pools to 2 from 20 and increased pool size to 90GB for a 124GB ram server. I've also enabled file_per_table. What is bugging me is the constant spikes in disk read/write speeds. Picture below is while the server is under decent load (file parsing into db) and it has been up with the updated config for about two days.