When the bike was assembled, the technician should have put grease on the pedal threads. They sometimes don't do that. When there is steel threaded into an aluminum part, they can corrode together making it difficult to remove. This may be the source of the bad threads. It has happened to me as well. So, cleaning out the threads and applying grease to the pedal threads will be a good step to getting things back together properly.

As for the tick, you are probably right, it might still be there. Check to see if the crank is hitting something. It is not likely if it happening at 12 o'clock, but check anyway. Check for play in the crank. They let us know what you find.

Good luck. Feel better.