I recently got an SCT tuner and I am waiting to get a cold air intake as well. I installed the strategy tune with 87 octane in the meantime to get the cold air intake so I can see how it drives with just the tune. The problem is: even with the 87 octane tune I get pretty bad detonation after then engine warms up, the car also feel sluggish and slower than the stock tune. I returned the car back to stock for now and there is no detonation at all and the car performs better. I live in Calgary, Alberta and the elevation is around 1100 meters here and over 2000 meters when I drive to the mountains, I use 87 octane gas and even from what I read with the altitude I could tune the car as if I use 89 octane so i'm even more surprised I get detonation with the 87 octane tune.
If your car runs normal without tune, and acts up when you have tune installed I would start by looking at the tuner first. Did you get a custom tune loaded to the tuner where your suppose to be running an aftermarket CAI?