I'm starting this just as an FYI. I searched around a bit and didn't find a thread about this specific topic. Hope it helps out a bit in case the subject pops up.
I recently went in to get an emissions test on my 2006 (1GR-FE/4.0 V6), Arizona required after 2006. I was unable to get a test done because the computer reported OBD II system "NOT READY".
I recently had my battery disconnected and come to find out that it takes 50-100 miles (per the dealer) for the computer to reset. I drove about 67 miles highway and stop and go; went back in to get tested and it passed no problem.
Anyhow, just as heads up in case someone runs into the same problem.
-If you're interested, let me know and I can post the read out too.