06 auto with reman engine less than 2k miles on it. Two times with this new engine when I have missed a yellow lights and have had to brake hard to stop at the intersection the car stalled. Battery is a optima red top and about a year old, both times I was running nothing that required additional power (radio, lights, heat etc). Coils and plugs have less than 6k miles on them. Any ideas?

 

Vacuum leak?

 

I have an AEM CAI, vfad is capped. Maybe when the dealership put it all together they loosened something? Idle is fine so I don't think its that.