OP, I think you've already turned this into a worst case scenario in your head. All anybody on this board can do is suggest what the problem might be. You need to take this up with the manufacturer only. Clear your head before you call and have a real conversation with somebody with clout there...
Yes, it will fit. There is also a little extra clearance for an air filter. I actually have 2 of the cowl induction air cleaners, but they aren't free. You should be able to use my existing harness to connect to your fusebox and have operational flaps when you floor it.
I installed a new cowl hood on my 80 Z28, and the original is now just in the way. It's black with orange highlights and shines up nicely. I'll give it to anybody willing to come get it. I'm in Pelham, Alabama, about 20 miles south of Birmingham.
I watched it, but it doesn't really go into positioning the clips. Somehow, the guy is able to adjust his clips when they are already attached to the panel without them getting stuck or falling out or causing other clips to bust loose. I wish it was that easy.