How long does it take for the engine to reset after reconnecting the battery. I have an 06 Mustang. The battery died so I replaced it and then flashed a new code so I could pass emissions with the SCT x4 tuner. What factors affect how long this takes? Engine runtime, mileage or both? I ran it for about 70 miles and took it to get tested and it still hadn't reset.

 

Usually on a GT, drive it 10-15 minutes, drive it around at various speeds. Let is sit 6 hours or more (overnight), drive another 10-15 minutes and you should be good to go.
If you still have two or more not ready's, it could be because the tune has your rear O2 sensors turned off. But for a stock tune or a tune that is emissions ready, that should do it. On my V8, I get them ready on the 2nd drive cycle, on the way to the inspection shop.

 

The battery needs to be disconnected for 20 minutes or more. Depending on how "dead" your battery was, simply removing the old one and installing the new one without the wait time likely did not clear the adaptive learning and associated memory.

 

I think he's asking about the "drive cycle" to get all sensors "ready" for emissions test.

Here's a technical definition of the "drive cycle"... http://www.obdii.com/drivecycleford.html

forget about 1 & 2, you've pretty much done that already.