as @
FRSBRZGT86FAN said the oft guys don't cater for catted headers.
running the stage2 tune should not cause any major issues but you might want to log for knock
look at FLKC FBKC and make sure IAM stays at 1 and have a look at AFR and make sure it looks ok as well
If you do go back to stage 1 tune safest option you might still throw cel code P0420 for cat efficiency so it might be best to disable it in stage 1 tune using romraider. The stage1 cam timing is not going to be optimal as its for a fairly EL header