I have a PCV and Auto-Tune on my '08AE. I think it's great, especially if you change your setup later. I let the Auto-Tune run for a while then upload the changes to the PCV. At first the changes were significant, but as you get closer to the ratios in the Auto-tunes map they get smaller and smaller.
I am very happy with this setup and the bike is running perfectly. Hope this helps.