99% what? Space consumed? Utilization? Either way, you need to fix this instead of worrying about rebooting the drive (which is not something you can do properly anyway without rebooting the whole computer).
Have you scanned for malware?
I would also run Windows Disk Cleanup (or CCleaner if already installed) to clean out the clutter. And don't mess with the Windows default settings. It is highly unlikely you are more qualified as a computer scientist or engineer than those PhDs and CompSci developers at Microsoft. I sure am not. So re-enable SuperFetch and every other default designed to enhance performance you changed.
Is this the computer in your System Specs? If you have 64-bit Windows 8.1, you might consider bumping up your RAM to 8GB. This will decrease the need for Windows to bang on the hard drive's page file (which I sure hope you have left alone and are letting Windows manage it) near as much.
If you have 32-bit Windows, then 4GB is limit but the amount of available RAM will be reduced to ~3.2 - 3.6GB due to the way 32-bit Windows does hardware mapping in RAM. If you also are using integrated graphic then another large chunk of your system RAM has been stolen... err... is being "shared" for graphics processing. In that case, consider adding a graphics card. Not only will you most likely get a better GPU, but the card will have its own dedicated RAM, freeing up the previously stolen/shared RAM.
How much free disk space do you have? If very low, this may be compounding your problem too.
And while Avast is an able security program, it has been known to consume an excessive amount of resources on some computers. Since W8.1 already has the very capable Windows Defender built in, I would uninstall Avast and run WD. You still have MBAM to ensure WD (or you, the user and always weakest link in security) did not let something slip by.
FTR, WD and MBAM is what I use on all my systems.
