did you ever figure out what was wrong?! I’m having the same issues with my 99 Tacoma right now! It’s driving me insane! I’ve in the past replaced all three coils, and changed 1 & 5 just to make sure it’s not bad again. Done spark plugs and wires not too long ago, and did the cam/crank sensor when I had a misfire in the past (2 & 5) From what I’m reading so far I’m leaning towards injector.

 

99 up seem to have an issue with injectors after 20 years here and there, lots of threads regarding this, and many much more recent than 2009.