I dont even.....
The PCB is the printed circuit board, so as far as upgrading from iOS3 to 4...that doesnt do anything physically to the phone. The reason the heat gun or oven tricks work is because it physically heats up the solder used inside the phone making better connections. For a program to do this it would have to essentially just make the phone run incredibly hot (hot enough to have the solder run, which is up there).
In short..no there is no way to make a program to reflow the PCB in the iphone....