My first guess in what’s happening to you is you got some blowback on a rail and it’s jamming the Y axis. When cutting 1/4 inch or more it’s a real hazard and you have to watch out for it. Check the rails for smoothness. The limit switch throwing alarms is just a byproduct of the lost steps from the jam.
I think I must have dodged whatever firmware update caused the issues. I know I updated, then didn’t cut for a while. When I did, I got the torch firing error and found this thread to re-update to 1.3.