just go and download supersu app from google playstore and installed it
if you wish uninstall kingroot or just let it stay - nothing wrong having both on phone
I will recommend limonchelo rom - really problem free especially good for newbies like you
I had read of so many issues users faced on other roms including stock roms but most doesn't even wish to try this rom. They however love to continue to troubleshoot their issues and trying to update to latest versions

Skip the root step n proceed straight to install custom recovery using fastboot flash
What malware - I don't see any? Any app you don't want just uninstall using titanium backup since phone is rooted
Don't install any unofficial app through unknown apk n you will avoid virus into phone. Download all app from playstore. You never know which app will give you malware/virus issues from non official app