Hey man -- not trying to be difficult or anything, but I did actually say I'm running manual software on the auto ecu (which works totally fine and is also what the OP was asking about).
This will be less crap than the other way around, but your idle, warmup and gear detection is far from good.
It's just a question of standards. What maybe "totally fine" for you, is horrible for someone who knows what to look for.
I don't see the point in the entire cross flash fad. You take a car, you read the SW, you tune the SW and you put it back in the car, done.
There is never any need to change it to something else.