Macbook Pro Mid-2010, Yosemite 10.10.5 left (primary) mouse click does not work on Apple software

Hey,

This is driving me crazy! I have a Mid-2010 15" Macbook Pro with Yosemite 10.10.5 running. My left mouse click (primary) has stopped working on every Apple software (except Safari and iTunes). I am able to use the keyboard in all of those softwares and also the right mouse click (secondary) does its function in all those softwares. I also use a Bluetooth Magic Mouse and a Wacom Intuos Tablet. The issue is the same while clicking with a Trackpad, Magic Mouse and Wacom. I usually have a Belkin USB splitter connected connecting two external hard drives. The problem is software only since the left mouse clicks work as usual in the Guest Account.

The softwares include the App Store, Mail, Messages, Notes, Calendar, Reminders, Contacts, Pages, Keynote, Numbers, Microsoft Office 2016 (the 2011 version works).

Here are the things I have already tried and failed.

1. I have tried reinstalling the OS. Twice.

2. Reset the SMC and PRAM multiple times.

3. Have made sure that my bluetooth mouse isn't accidentally pressed.

4. Have uninstalled the Wacom driver.

5. Have put the (com.apple.) mouse and trackpad preference lists found in the Library/Preferences/ in the trash and restarted/shut down.

6. Have put the App Store preference list in the trash and restarted.

7. I have found that my Disk permissions have conflicts. I have tried to repair them but when I verify the permissions after repair, the same conflicts show up.

8. I have tried formatting my hard disk and restoring from a Time Machine Backup.

I should mention that all other software do register the left and right clicks. I have an issue with my NVIDIA graphics card. Apparently it's a known problem with 2010 MBPs and Apple had called a replacement program that I missed. It is because of this that my system restarts randomly in the middle of work and I suspect that has led to corruption of my data.

I really need help to fix this and cannot afford to do a clean install.