I actually tried this with a set of JBA Tunda Headers (P/N 2011)...
The problems that you have is that you dont have enough room to run larger diameter primaries due to the clearance issues already previously mentioned.
The only way to really gain anything would be to use a thinner wall thickness and keep nearly the same manifold profile. In addition, by running larger primaries you would want to put a longer initial run in that primary thus creating more of a 120 degree header design. A shorty header and nothing like a more power producing long tube design would need to be used as with the 2uz out of the tundra and sequoia.
If it can be done (i have my reservations to it) it would also have to be a 4-1 design instead of a 4-2-1 design to maximize clearance. The left side has issues with the steering rack and the right has issues with the ladder cross member and the frame rail.
The 4-1 design would be great for those of us living at WOT but those interested in better low end torque and mid range power would be left as a 4-1 design is really optimized for that in the upper rev band and at WOT. Dyno plots of the 2011 headers on a 2005 Tundra show gains starting at about 3500rpm (or more than half way up the rev band).
the #-1 design is the same as seen in the engine setup above except this time its a 3-1 design and looking at the dyno plots you can see that at about 3500rpm the headers start making power and go to redline. While the larger diplacement of the 2uz engine would benefit more than the 3.0I-6 of the Ie300 but i think those looking for more power from towing are going to be disappointed.
If these guys are willing to try, im down for it. Taking out the 3stg cats would also need to be done as im almost positive that you could pick up fairly decent power just by removing the twin cats and running a single high-flow metallic substrate cat.
Im sure that I could have modified the tundras to work but with out all the proper tools for the job (dyno, mandrel bender and the like) I dont know how much it actually would have gained. In addition a new car to play with and an increasing work load kinda diverted my interest in the project.
Here is the article of the Tundra with pictures of the OEM manifolds directly next to the 2011 JBA shorty headers.
http://www.jbaheaders.com/articles/4wdsuv_1005.pdf