Possible to make manual swapped 1997 Jeep ZJ stop looking for its auto trans?

Thinking about buying a ZJ from my brother that has had an AX15 swapped in to replace the 42RE or whatever it used to have. Problem is I live in an area that tests emissions (but for whatever reason doesn't do safety inspections) so I can't have any codes being thrown (as they currently are) when I bring it in. And some extra performance and fuel economy would be nice too.

Is the software capable of making the JTEC ECU forget the old auto box?

Thanks.