Don't don't mess with your stock air box, without it filtering properly your motor will soon be toast.
The 2 resonators in the intake pipe before the air box are mainly for intake noise reduction. If you remove them
plug the holes or it'll suck in dirt.
"there is a smaller tube coming off the intake piping." Yes you need that or you loose your idle speed control, as well as A/C idle up.
With Pod filters the problem is they are hard to mount securely, and they tend to suck in hot air.
There is also an intake air temp sender mounted in the stock air box, you'd need to fit that too.
Toyota
really made it had for people who want to change things, ha ha.