Now that I have fixed my problem (on my own), I will make this a thread where everyone can post problems like this. I will show causes and any fixes if possible. My original problem happened when my CPU heated up, which bottlenecked GPU but fixed by turning off hyperthreading. Virus-caused issues are not posted here.
Causes of Slowdowns/Bottlenecks and Fixes:
Low-end/faulty hardware FIX get new hardware
GPU Heating Up: FIX Dont OC, check cooling, check power supply
CPU Heating Up: FIX Turn off HT, check cooling, dont OC, check power supply
Software Conflicts: FIX figure it out youself
Bad Drivers: FIX Rollback or update drivers
Slow Hard Drive: FIX Check some BIOS settings (sometimes changes itself), defragment, free up space
Causes of Slowdowns/Bottlenecks and Fixes:
Low-end/faulty hardware FIX get new hardware
GPU Heating Up: FIX Dont OC, check cooling, check power supply
CPU Heating Up: FIX Turn off HT, check cooling, dont OC, check power supply
Software Conflicts: FIX figure it out youself
Bad Drivers: FIX Rollback or update drivers
Slow Hard Drive: FIX Check some BIOS settings (sometimes changes itself), defragment, free up space