coils are common to go out in all the V6's.
Swap the coil with another cylinder and see if the misfire moves with it.
I am curious to find out what happened when you moved the coils around. I have an 04 SR5 and I just had a coil go bad. Took it to mechanic because I was in a hurry to get it fixed and they charged me $300 to change one coil. Drove it away from mechanic and same problem occurred. Took it back to the mechanic and the found the gap in spark plug was .80 (pretty far from .44 required) they re-gapped it to specs and it is running fine. I am thinking about replacing the coils when I change out spark plugs.
I am curious to find out what happened when you moved the coils around. I have an 04 SR5 and I just had a coil go bad. Took it to mechanic because I was in a hurry to get it fixed and they charged me $300 to change one coil. Drove it away from mechanic and same problem occurred. Took it back to the mechanic and the found the gap in spark plug was .80 (pretty far from .44 required) they re-gapped it to specs and it is running fine. I am thinking about replacing the coils when I change out spark plugs.
Why are you going to replace all the coils? I would also request my money and old coil back from that shop.