Some progress and setbacks.
I was able to remove the 2015+ IRS differential pinion flange with the help of the Factory Five provided pinion flange to driveshaft adapter and a ratchet strap to keep it from spinning on my. I followed the instructions pulled from dhuff's Mustang GT repair manual. First I tried to measure the free spin torque of the flange which is under 20 in*lbs and then I removed the nut and flange itself with a puller. Not too difficult, but the procedure Ford uses is to punch the nut and stake it into a recess in the pinion gear. Great for holding it place from spinning, not so great to undo.
Next, I tried installing the 03-04 Cobra flange on the new Super 8.8 differential and found it's a no-go from stock part to stock part. Can you see the reason?
Ok, neither could I. After measuring with some calipers, I found the spline diameter is just about .030" smaller on the Cobra flange even though both are 30 spline 8.8" pinion flanges. Dang it!
I put out a request to Nitro Gear and they won't do a Cobra flange with a 2015+ Mustang GT spline even though they have the tooling to do both. I've also got a request in at a local company to see if they can modify the splines. I really would prefer not to have to modify the splines myself.
Any ideas of places I can contact to make the correct splines even if I have to turn my own flange on a lathe? Even better, a company that might be willing to modify the existing splines?