OS troubles after disconnecting dying secondary storage only HDD from system

[namenlos]

OS on SSD, installed a secondary HDD weeks after install. It has been running great for about 6 months.
About 2 weeks ago, my computer started to really slow up. I ran crystaldisk info yesterday and it reported that my HDD had close to 200 "uncorrectable sector counts." It also listed the drive as in 'Caution' With some research, I realized the drive was on its' way out. So, I copied all of my data over to an external drive and proceeded to disconnect this dying HDD from my system.
It seemed to boot up fine, but I soon noticed that I couldn't open my file browser nor Computer / Control panel ...etc. However, I could open up Chrome and other programs just fine.
I'm at a loss for what's happening.
I used the computer for weeks with SSD only before putting in the HDD without any issues. Why am I now having problems with the dying HDD disconnected?

All help is much appreciated!

My rig-
Windows 7 64 bit
SSD- Crucial 250 GB
HDD- WD Black 750 GB
12 GB RAM
AMD X4 955 3.20 GHz
AMD Radeon HD 5700

 

[digitaldoc]

It sounds like some data was going to the HDD, although the default should be to go to the boot drive which was the SSD.

May need to uninstall and reinstall Chrome and the other affected programs.

I would probably get a new HDD installed, and reinstall Windows for a fresh start.

 

[BadAsAl]

What does it say when you go to Properties on the SSD and click Check Disk?

 

[Joseph DeGarmo]

Make sure that you are not installing any programs to the HDD, including Steam and Origin. Game folders can be installed onto the HDD, though.

 

[ArtPog]

Could be a myriad of possible problems affecting the OS. The HDD is now out of the picture, right? So we're not dealing with that situation, right?

Just as a preliminary step it probably would be wise to test the health of the SSD just on the off-chance something is amiss with that device. Or have you already done so?

And if you haven't already done so check for firmware updates from Crucial.

Probably a good idea to run sfc /scannow and see if system files may be corrupted. I assume you're familiar with that command.