Ya of course you can & why would a clean installation of windows mess up your PC ? you can always do a clean installation of windows anytime you want because sometimes you feel registry is messed up or Windows is damn slow .
use windows 8.1 Core its lite & good & pro is gr8 too , doesnt matter
Get the drivers you want from MSI site .drivers like Chipset , Intel's Integrated VGA driver , Sound , USB ports & ...
But get the Nvidia VGA driver from Geforce.com & try to use WHQL ones & always stay updated with your Nvidia drivers to get the best out of your VGA .
& if by saying bloatware you meant Windows 8 pre installed apps . it comes with windows 8 & there is one POWERSHELL command to get rid all of them . first run PowerShell as Administrator & then paste "Get-AppxPackage -AllUsers | Remove-AppxPackage" & there ya go