MWBytes didn't fix it. I could boot in to safe mode.
I ended up fixing it by running startup repair after significantly editing the registry. I removed most of the traces manually, but some of the still persisted. I was able to get in to the task manager again, which helped, but even after a full scan with multiple programs it wasn't being detected.
It was actually a pretty interesting piece of malware. I have no idea where I downloaded it from. It made it through my firewall(and I use a good one) at about 9:15 pm, and then it waited in my temp for about an hour before striking, so that it could cover the file it was from.
It also used a two randomly generated .exe files, so that it can be less likely to be picked up by programs like MWBytes and things like that. With the random naming on the .exe files, it's harder to categorize.
I ended up being able to run a system restore through the start up repair. Like I said I wasn't overly worried, I still had full access to the drive from my other Windows partition as well as access to everything from my Linux partition too.