Just because you measured the blind holes depth with a wire does not mean that the threads have been cut all the way to the bottom of the holes.
They are blind after all and their taps can't cut all the way to the bottom of the blind holes.
Run the 4 corner bolts in by hand and snug with a wrench to see how much of the bolt is sticking up over the head before the intake goes on. If you are at 3/4" it's gonna be a problem.
