[V8] 5sp VS Auto 3.6 ECU differences?

[Ron Wainwright]

Is there any differences "internally"?

It has come to my attention that the 3.6 Auto ECU doesn't cut the fuel off like the 5sp ECU... 
... It was told to me that in his 4.2 original 5sp car with 3.6 ECU and wiring that with the Auto ECU on deceleration he got smoke out the rear pipes..... but when he put the 5sp ECU in it didn't smoke on deceleration....does that make sense?

 Ron
91 V8 5sp mit 4.2 aka Black Betty (hibernating)
91 20020vt 22psi