Check engine is showing a code that displays a misfire on cylinder # 2 on my toyota tacoma 2001 that has the 3.4 V-6 (5VZE) engine, so far I replaced sparkplugs wires and sparkplugs, this engine does not have a distributor, it comes with coil packs for the spark plugs and the computer controls the spark, what else can I check that may cause this misfire on cylinder # 2

I would replace cylinder 2's coil pack.

What you do is swap the coil pack to a different cylinder and see if the code follows to that hole. I've seen a few where they leak spark and arc against the plug tube. By lifting it slightly while running, you may be able to see it.
Could also be a lean injector spray on that cylinder, but I find that rare. This is where I find a scan tool my best friend. Good luck!