Mac Mini with lots of I/O errors and related issues, trouble identifying culprit Setup:
Mac Mini 2011 with two drives:

SSD with OS X Yosemite and admin account home folder
HDD with my user home folder

Symptoms:
It began as many months of seemingly random slowdowns/beach balls, but the issues would go away (often after reboot, Safe Boot restart, or reinstall of OS X) then resurface periodically.  Recently (last week), problems escalated to being completely unable to login to my user account (logging into the admin account works fine).  When I try to login to my user, the loginwindow process crashes and it returns me to the list of users.
In Console, I’m also seeing lots of 'kernel: disk1s2: I/O error's (this is the HDD with my user home folder).  By lots, I mean it ranges from 1 per minute to 1 every 10 minutes or so.  Obviously the 3 big suspects are the HDD, the SATA cable, and the logic board.
Troubleshooting:

From the Admin account, I created a new user account stored on the
HDD.  I have been able to login to it, but it is exhibiting similar
symptoms to what I observed in my primary user account (extremely
slow, lots of beachballs).
I reinstalled OS X and tried multiple Safe Boot reboots (both of
which have previously helped when encountering slowdowns and random
beach balls).
I replaced the SATA cable with no improvement.
I removed the HDD and used it as an external USB drive on another Mac
and was able to access/scan the whole drive with no observed issues
or slowdowns and no I/O errors.
Disk Utility ‘Verify Disk’ comes up clean every time and the
S.M.A.R.T. status is Verified.
I ran the Disk Warrior hardware test and it said the drive is
functioning normally.
I ran the Apple Hardware Test (Diagnostics tool) multiple times (both
quick and extended) and it has never reported any errors with the
drive, logic board, RAM, or any other hardware.

It sort of feels like a hard drive problem, but I have no proof of it.  Since everything else comes up clean, I'm left with the logic board, but no way that I know to test it other than the Apple Diagnostics tool (which shows no problems).  I’d hate to waste money on replacing the hard drive or on repairing the logic board without knowing which is failing (if either).
Any suggestions on further troubleshooting steps, particularly to determine if it’s the hard drive or the logic board?
Side note - yes, I have backups to restore from :)
Thanks
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.