Mac Mini with lots of I/O errors and related issues, trouble identifying culprit
Look at something like Scannerz because it was designed to find those types of problems. Here's a link:

http://scsc-online.com/Scannerz.html

Scannerz is fault detection software that monitors and looks for signatures associated with various types of logic board, drive, and system failures. I suspect either a cable, connection, or logic board problem.

I hope it's OK for me to post that link and info.