We call that a parts cannon. I had an 07 Honda Civic that I chased a fluctuating idle on and what finally fixed it was replacing the valve stem seals, essentially caused a vacuum leak. Not an easy job.
How many miles? Regular maintenance?
The codes wont just go away you need to clear them with a scanner, random misfire is likely from air in the system especially if you aren’t getting heat from the heater.
Did you disconnect the battery at all? That would explain the windows not working there is a relearn procedure something like hold all of the buttons from the drivers side controls or each individually at their respective door switch I dont remember exactly I used to just fumble through it until they started working again
Second this, air in the cooling system on newer vehicles can lead to a poor idle the system actively uses the coolant temperature to determine how it should run if air is passing by the sensor it will momentarily read at a different temp.
Fully cycle the key in the ignition several times
I found this answer on stack exchange for an 09 - “Resolved (so far :) - last week replaced the timing chain tensioner (Toyota OEM #1354037030). The noise at low load is now gone and the RPM needle remains steady at idle.”
https://mechanics.stackexchange.com/questions/67722/corolla-idle-fluctuation-and-noise