Wesley Law

I have an 07 2500 hd nbs with a ly6. We did a vvt delete and a trickflow sloppy stage 2 cam swap. After the swap we started it up with the vvt disabled using hp tuners. It cranks and runs but after about a minute and a half the check engine light gos off and comes back on and it shuts off as if i turned the key off. Im confused because it finds idle nice and runs without a hitch. Has anyone ever experienced anything like this before? Any thoughts would be greatly appreciated!