02_GT_5Spd, the cutting on the bumper is something I totally didn't even consider during our other exchange on the IC issue!
I was very fortunate that a good friend of mine, and engineer, did the Stage 2 on his 2012 BOSS 302 (with the help of another mutual friend who is an engineer!); they handled the install of my P-1SC-1 Stage 2 while I sat on the garage floor eating pizza and drinking beer! One of the things that got them slowed up on the 2012 BOSS 302 was reinstalling the bumper cover after putting on that Stage 2 IC. They had to hold it in place, then trim a little off, then hold it in place, then trim a little more off, then hold it in place...
...you get the idea.
When it came to my 2014 GT, the bumper cover just went right on!
If I were you, I'd consider looking for a stage 2 IC out there somewhere maybe used??? Or some other aftermarket options? For instance there is this: Mishimoto Universal Mustang Intercooler M Line MMINT-UM (79-17 All) - Free Shipping
The thing is, I don't know what it'd take to get the piping sorted out to make it work with your ProCharger. And if I member correctly, the P1-SC-1 has the MAF installed into the outlet side of the IC; there is no provision for this with the linked IC (I think). So you'd have to figure out that with the piping.
And it looks like you're right; they did change the design of the new HO IC for your kit to a taller skinny IC.