Computer Extremely Slow after changing BIOS setting

I was having a problem with my computer going into sleep-mode and not being able to come out without unplugging it. So after a quick google search it looked like I needed to change a bios setting so that my computer would recognize my keyboard and mouse when it's in sleep mode. I couldn't find the right setting but that's aside the point. I also noticed a PCI-e frequency setting. I googled what that meant and my curiosity had got the better of me. Someone had recommended it be at 107 rather than the default 100, so i tried that and started my computer. From that point on I've been having serious problems. My computer is extremely slow. Most of the time after I log in it goes to a black screen with a mouse, and sometimes it'll start up fully but it'll be extremely slow and then I'll get the blue screen of death after awhile. The only thing that works is starting up in safe mode. I've tried changing that setting back to 100, restoring all BIOS settings to the default, a full virus scan, a system restore, made sure my hard drive was in DMA mode. I'm not even sure it was the bios setting that caused the problem. Could something be wrong with the hard drive? Does anyone know the problem or have any suggestions?

Windows 7 64 bit

Western Digital Caviar Green WD15EARS 1.5TB 64MB Cache SATA 3.0Gb/s 3.5" Internal Hard Drive

AMD Phenom II X4 965 Black Edition Deneb 3.4GHz 4 x 512KB L2 Cache 6MB L3 Cache Socket AM3 125W Quad-Core Processor

ASUS M4A88TD-V EVO/USB3 AM3 AMD 880G HDMI SATA 6Gb/s USB 3.0 ATX AMD Motherboard