I've always had great luck with crutchfield.com. They have fitment guides, and factory style connections to make everything a breeze. The stock JBL speakers are okay, but a cleaner amp can make them sound better. I'm sure you'll find the separates you're looking for, with the quality you want. They might even have the JLAudio center console sub still?? I know I've also seen the JL Audio rear sub for the Sequoia that fits in the rear drivers side compartment.
Installing a new set of speakers in your doors may also take some modification to fit the plastic mount. When I had my door panels off, I also installed some dynamat to calm down some of the rattles. Good luck..
I'm getting the idea that speakers are not an easy thing for the sequoia!!! What component set up (brand) are you replacing the factory speakers with ??