The 2 forward mounting points on the 1999-2004 IRS-equipped Cobras have 14mm holes in both the chassis and the steel crush sleeve of the OEM rubber bushings. But the 1979-1998 Mustang chassis has 12mm holes to secure the rear lower control arms to the chassis, which is also used as the forward mounting point for a Cobra IRS subframe. Thus, when swapping the 1999-04 IRS cradle into a 1979-98 Mustang, you have to deal with the car having 12mm holes to bolt the subframe to.
Do not use the stock rubber subframe bushings, as their 14mm holes allow the subframe to shift relative to the chassis. That can cause noise as the subframe shifts, and any shift will change the rear wheel alignment.
What you need is some sort of adapter to connect the 14mm subframe mounts to the 12mm car. MM has exactly that, our urethane subframe bushings (MMIRSU-2). These bushings have the correct steel crush sleeve for 12mm bolts. This bushing kit matches everything up to work right!
For the rearward IRS subframe mounts, MM has low-profile bolts that offer increased tire clearance.