I tried running sfc /scannow
First off, never use SFC on Atlas. Thats how you can break your install.
Secondly, this might be something on startup causing the issue. I would recommend running the script located at: Atlas Folder, Troubleshooting, Safe Mode. Run the script Safe Mode with Networking. It will then ask to reboot, do it in a way that suits, the next time you restart it will enter safe mode.
When in safe mode, check if you experience the same issues you described.
When the windows JUST STARTS I can open programs and task manager, after a few seconds the madness starts
First thing is check Task manager and disable anything that is in the startup tab, there may be something that may be causing the slowness once you login.
If you installed any sketchy programs before this happened, this would be the perfect time to download Malwarebytes (Please note it may detect some scripts in the Atlas folder as malicious. However, they are crucial for making the other scripts work properly, so please ignore them if you can.)
While you are there, I would suggest you disable search indexing, as this may be the culprit of the slow response time.
Once done, go back to the same folder as I described, run the Exit Safe mode script and reboot, it should be fixed now. If not then you may have to reinstall Windows, but I would wait until 0.3 is released before you do so as a lot of bugs have been fixed such as what you are experiencing.
Bluetooth ( that still not working )
You will need to install drivers for it using SDIO once you have resolved your issues.