Thanks! If you had memory shortage, the cache numbers would be small, and if paging a lot, the si and so columns would be large. But this is not so.
We do see a big peak in bi and bo, which is typically disk activity. I wonder if something somewhere is building or repairing or scanning something.
Perhaps try running
ps auxrc
every five seconds for a minute or so, to see if you can catch a busy process in the act.
There are other utilities which might not already be installed: perhaps search for “How to Monitor Disk IO in a Linux System” or similar.
It’s worth noting that if you have doubts about the integrity of your system, rebuilding it from a backup might be the swiftest way forward. But be sure to have an offsite copy of the backup, if not two, in case of accident. And, ideally, do the install on a new instance and keep the existing one around until the new one is working OK.