Happy to say the car is back home and seems to be sorted. Read the description in the picture of my invoice to see what was wrong. The issue should be sorted for good this time, unless excess sealant made its way somewhere in the rebuild too.
Edit: Two weeks after the new short block, the engine started knocking again and this time the traction control and abs lights came on with the check engine light. Toyota offered to buy the car back when I asked to start the lemon law process.