The bottom end on the 3x00 V6 is pretty robust. It can safely handle 300 HP, maybe more. That's probably more HP than your iron heads will allow, unless you really crank up the boost.
If you put the iron heads on a stock 3400 bottom end, your compression ratio is going to be horribly low. It'll probably be less than 7.5:1.
Keep in mind that a turbo isn't a magic wand that you can use to make the laws of physics disappear. If the heads are a flow restriction when naturally aspirated, then they will also be a flow restriction when turbocharged. You'll just need more boost to force the air through them.
The 7730 ECM works just fine with the 3x00 ignition system. I know from personal experience.