Forgot about this post.
Well looks like it fixed it self in a way. I messed with the ECU tune and changed things around to see what it would effect, and it does not do it anymore. A/F stays constant now so I guess what ever I messed with fixed it. Wish I could give a more direct reason to why it stopped but it is fine now.
Everything runs awesome now. I did a retune for the water/meth injection and it has so much more power. No problems @ 18-20psi in the summer with 91 octane. Knock light is at setting 7 (10 the highest senstivity) and it only blinks a little bit at night and when I shift. I have drivetrain noise so I think it picks it up some.