Swap your coils and see if the miss changes cylinders. Chances are you got a coil going bad we've replaced a bunch of them for mis-fires.
this is about the best suggesrtion ive seen, seafoam wont help, its not a clogged injector
toyota has codes for injectors, a misfire is seperate. it is actually as simple as it sounds-#3 is not firing
check coil packs, all wires going to coils, make sure that if you swap em around you remember wheich is which,
toyota also will flag misfire if compression is abnormally low in a cylender
