The 03 and up 4Runners have three CATs. Two pre-cats off each header and the Main CAT where the two pipes eventually go into. Removing the two pre-CATs would be ideal in the event you want to upgrade your headers and have some substantial gains. Just getting different headers like the JBA if they even make them for the 03 and up 4Runners is not IMO worth the $/hp on such a large displacement engine. You would need to get two O2 simulators to keep from throwing a code. Technically you will still retain the Main CAT.
The other option and I have explored this is to have the two Pre-CATs moved back as far away from each header as possible. This gives you a long-header effect for the exhaust gases and will yield some gains.
Anyway I know this is one of my first post, but I been modestly modify for some time now. I've pretty much finished my Corolla and I'm working on my 4Runner. I'm sure you guys will see more of me around!