[LMH]

I'm not an FFR MK IV expert but on the older models, you need the IRS cage and suspension. Did your's come with the cage?
You can use the differential and CV joints out of the Mustang set up. The diff should be aluminum if it's an 03 Cobra Mustang and the inner CV joints are 31 spline. You'll need knuckles from a Thunderbird/Cougar as well as brakes I think. Not sure about brakes though as you may be able to use the Mustang brakes.
You'll also need to swap out the axle center shafts for the correct length shafts. They are available from FFR I think as well as a couple after-market suppliers.

Maybe one of the FFR guys with more knowledge about the MK IV will chime in with better info.

Good luck with your build!
Larry