Windows will start up but not allow program use

Although, my computer may be an odd setup and I am trying to resolve this problem by any means that does not involve spending $70-$150 reinstalling a brand new operating system. Below is a history of events that led up to my problem yesterday.

I initially had a HP Pavilion dm4-1265dx laptop (with a HDD running Windows 7 Home Premium), after a slight problem, I had to get a new drive because Windows said my hard drive was failing. After transferring the files from one drive to the other, I decided to upgrade to Windows 8 with a student discount at my college. I purchased the software online and upgraded my laptop's OS. After a while, my computer wasn't operating efficiently enough for me and I decided to upgrade it for the time being. I purchased a Samsung SSD and some RAM for the laptop while I got the money to get a desktop. Migrating the files from the HDD to the SSD wasn't a problem at all and everything was fine... for the time being.

I later had a slight problem with a program that I use (for some reason the name escapes me) and refreshing the computer was the only solution. I was strangely only able to achieve this by taking the recovery disks of my laptop (Windows 7 Home Premium) and installing the OS onto the drive. Then I upgraded the OS by reinstalling the Windows 8 onto my computer.

Later on, Windows 8.1 was released and I proceeded to upgrade my OS yet again. It was successful - again no problems. Not too long ago, I purchased a Lenovo K450 desktop and put my SSD from my laptop into my desktop. Wanting to use the 1TB HDD included with the computer (along with Windows 8 installed) as a media drive, I decided to format the entire drive and used my SSD as my active partition. I had to validate Windows by phone which granted is a right of Microsoft to do, but again no problems.

It wasn't until yesterday that my problem started, I was making stuff for nachos and I wanted to talk to my friend via Origin's chat system (which for some reason doesn't like my Surface Pro), I decided I would remotely connect to my PC from my Surface and keep chatting. Once I finished cooking my dinner, I went back to my computer and logged in to find my resolution was out of wack. I remedied the situation and restarted my computer. When I logged in, it showed my background and my taskbar (only the safely remove device, network status, and time notifications showed up on right, though many more are supposed to be there) and no desktop icons showed up.

Basically, my desktop is and is not working. It will make it past POST and allow me to login but will not let me run any applications. I am absolutely positive that the problem is not virus-related. I just need a solution that can remedy my situation. I have tried to use the Windows 7 Home Premium Recovery disks, but it obviously didn't work. I also have tried talking to Microsoft support regarding this and they couldn't help me.

I am able to open the Windows Explorer window and the Run prompt, but cannot open any applications (including task manager) or right-click anything to bring up any normally available menus. The best it seems that my computer can do is open command prompt and show the last tabs I had open in Chrome (without showing the pages themselves).

Any help in the process of fixing my dilemma would be greatly appreciated.