I removed them with a PCIII and still recommend you leave them in there. No amount of tuning got it as smooth down low as it was prior. Up top, didn't notice any change. My mph on the track didn't go up or down at all and suggested no change in power up top. Not worth it.
ETA: This subject has been beaten to death. Try a search...
I did it on my first 04 seemed to have way better throttle response and I think it was faster because I was worried about it running lean with no pc so I put them back in after a month or more and was so dissapointed I sold it!:lol:
I pulled my secondary butterflies in my first gen 1 and put a PC3 on it with a dyno tune. Didn't notice the difference before/after. On the second gen 1, I left them in and still didn't notice the difference. I'd suggest to leave them in. Just seemed like more work than it was worth (mine didn't come out easy).
I pulled the secondaries on my 04 with just a slip on, no pc or anything and noticed greater throttle response all around except it seemed to lean it out too much on the bottom end when you hammered it, so i put them back in