. . . DTCs P0420 and P0430 are usually set to "no error reported" rather than actually turning the sensors off.
I'm pretty sure this is technically correct; and it causes the same problem with emissions testing for practical purposes.
I am not sure about the exact codes that the OP posted but it sounds related to me.
Unfortunately if you can't get anywhere with the Bama tune, you'll have to put it all back to stock. Or check with Steeda to see if they have an insert for that CAI that will allow you to run the factory tune long enough to get the emissions done.