I have no clue and think that is the wrong direction I pointed to!
The picture above was made with the old version of Sineos excellent “Graphstats webpage” tool. You may try the new version, which has much more features https://klipper.discourse.group/t/rework-of-the-graphstats-webpage.
I think you see the error very good here (pink)
I spend an hour now to find anything curious in your latest klippy.log. Not much success
Line 3237: "Timeout with MCU 'MKS_THR' (eventtime=2342.829690)"
is the error before. “Could” point to the CAN bus?
You might follow Sineos “Knowledge Base” https://klipper.discourse.group/t/missed-scheduling-of-next-digital-out-event. First thing I would do “Disk errors / dying SD card” try a new one since it is the easiest and cheapest thing to do.
Again, good luck!