Okay, after several weeks I ended up doing several things to try to fix the issue.
Circumstances made it so I swapped out all 8 drives and I put in 8 x 8TB WD Red drives. I reinitialized the entire NAS.
I ran it for a couple of weeks without issue at that time and decided to install Plex from QNAP repositories. It worked fine, so I upgraded to recent server version 1.16.5.1488. This is where problems started. The install failed and I got the data file error. I tried again it failed. From there I received the 404 not found error when trying to direct connect. I rebooted and tried again, from there it locked up mid update (stuck at 20% install for 12 hours). I finally just forced restart and apparently, the update stuck and runs with the current version.
I am currently running 4.3.6.1040 and recent PMS. But I am concerned about the longevity and frequent errors.
I can’t identify any hardware issues from kernel logs or anything else.
I have attached the logs I generated.
Plex Media Server Logs_2019-08-23_18-40-25.zip (2.7 MB)