I'm pretty sure you will find the major dimensions of your brembo rotor and the Baer rotors will be the same, with only the hat to braking surface transition area being different. The Baer rotors are very similar to the original KH rotors used on the 94-98 Cobras, and your rotor is the brembo sourced replacement used originally on all 99-04 cobras, Bullitts and Mach 1's.
Your setup will end up being virtually identical to the Baer kit, with the exception of the bracketry between the knuckle and the caliper anchor brakcet. Most likely your bracket will look exactly like the Baer intermediate bracket, except it will mount about 1/2" closer to the hub centerline because of the differences between the Baer anchor bracket and the OEM cobra caliper anchor bracket.