Some of those codes are odd, you shouldn't have AIR codes at all on a 2004 and the NV3500 doesn't have skip shift or reverse lock out solenoids so you shouldn't have those codes either. Almost makes me think you have a F-body tune loaded, but if that was true your DBW throttle wouldn't be working at all.

Also the theft deterrent learn mode code is a little strange. That should be a self clearing code after the key is turned off.

I imagine VATS was turned off, but maybe Allen will chime in with what he did for your tune. (I see where you said he checked it already now)