None of the thing you mention that you have done touched the user storage partition, that remained the same the entire time.
And your symptoms remained basically the same the entire time.
First target, always, blame it on the indexer.
Clear off all documents now stored on your USB accessible user storage partition, then do a full, cold, boot.
Wait for the system to complete its to-do list.
And keep it on a charger, the to-do list processing will stop when the battery is low.
Then continue testing for source of problem.
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