Here's an example of a subwoofer enclosure for your Tundra that fits under the rear seats:
2014-15 Toyota Tundra Crewmax Sub Box Under Seat Box I had NET Audio design and build a fiberglassed enclosure for a client of mine with a Dodge truck that has a similar issue of a lack of space for bass. It turned out amazing. They also can make an enclosure to go behind the rear seats if you have a Crewmax, but if you settle on big amplifiers you'll want that space for the amp rack.
We offer several speaker upgrade kits for the Tundra. 3-way components up front and 2-way components in the back can work great. It would be an upgrade above and beyond our
Stage 3 kit. Keep in mind we developed these kits with DIYers in mind, and a nearly factory original appearance can be maintained. If you will have A-pillar pods built the front speaker system should be upgraded to different mids and crossovers.
You have a lot to consider and I can refer you to a local specialist. Feel free to pm me.