The AP 6468 is a great turbo with a lot of potential. My buddy is running it and he dyno'd just north of 700hp on dual pumps.
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Correct me if I'm wrong, but that lag with a non vgt is normal. You should have contacted your tuner prior to selling the stage 2 and see if they could have adjusted the lower end to make up for the lag.
I don't know how the AFE flows but I would recommend a stage 2 over it. Gonna be pushing a...