There is a simconnect issue right now that is causing this.
It is supposed to be addressed in this coming update.
You actually found the temporary solution, which is the less you run through simconnect the more stable the sim is.
By dialing back the AI, you did just that.
Not using any external aps helps as well.
There are a lot of threads/posts in the forum on this issue if you want to search for more info.
I very much doubt MSFS hurt your computer as it doesn’t even use the registry.