Problems with my 2005 Mustang V6 4.0L, Failsafe Engine Mode

[jcorbin]

Need some help please! I bought and Installed the following items on my 2005 Mustang with the 4.0 L V6. SCT SF3 Tuner from American Muscle with the BAMA tunes and a JLT Cold Air System. Having problems getting the Failsafe engine Mode indicator to stop coming on. I have contacted BAMA and they have gave me a new tune and still the indercator will not go off. I tryed to clear the codes with the tuner but when I check on them again they are back. The two codes that won't clear are Uo300-Internal Control Module Software Incompatibility. and P1000-OBD System Readiness test not completed.