Black Screen with Cursor

I recently made changes to my parents' computer in order to help with the fans running at high speeds constantly. I used a tool called Simple System Tweaker, and disabled only the default visual and service tweaks. When I rebooted, the system was stuck on the black screen with the cursor. I did a hard shutdown and booted into safe mode successfully. I ran the MBR Regeneration tool and rebooted, but I got the same issue. I used the last known good config option in the F8 menu and got the computer to boot without the graphics driver installed. I installed the updated driver, then disable some startup programs and rebooted. Same issue.

Before I left for work today, I ran the sfc scan and found issues, and I also ran Windows AIO Repair which found errors on the drive. I scheduled the computer to run a chkdsk after the Windows AIO Repair tool finishes. Are there any other things that anyone can think to try? I won't know if the repair tool worked until much later. I just wanted to get more ideas as to things I could try before going in blind again. They are using an NVidia Geforce 250 if that matters.

Also when I went to Repair Your Computer in the F8 menu, the system could not run the startup repair, stating "If you have recently attached a device to this computer, such as a camera or portable music player, remove it and restart your computer. If you continue to see this message, contact your system administrator or computer manufacturer for assistance." When I tried the sfc from the Repair Your Computer cmd, it could not run because it said there is a pending scan.

UPDATE: I managed to get the computer working thru various hardware and software cleanup; however, there are now 3 fans in the system that have power--the led lights are on--but they are not spinning. I didn't notice if they were spinning before or not because I was too focused on the issue being software related. I've tried disconnecting and reconnecting the fans, but same issue. The way that the wires are running in the computer makes it difficult to know how/where they are connected to the motherboard. My fear is that I did something when I moved the computer out from it's location. Any help would be appreciated. Anyway, here are some things that I did:

- Cleaned A LOT of dust from the inside w/ compressed air
- Uninstalled needless programs
- Installed new lan driver
- Disabled unnecessary services
- Unplugged vga cable from monitor and only used dvi (they had both plugged into the system for one monitor)
- Installed Windows recommended version of the graphics driver
- Removed 6000+ useless registry entries
- Ran CCleaner
- Ran system defrag
- Ran SFC scan
- Removed 250+ infected files
- Ran chkdsk /r
- Updated bios

That's about all I can think of right now. Needless to say, I was working on this for about 9 hours yesterday. Also I just found out that the gpu was missing its fan. I heard a rattling in the computer and found the fan in the hdd area, but one of the blades broke off. Can it still be used?