After you enter the different injector sizes, your car should idle just as it did before. Back when I had EMB and swapped in 330cc injectors, it started right up and and required no tuning. There are no provisions for idle control in the EMB.
Your datalog looks normal, except that you want 11.8ish AFR for 8psi. You're dangerously lean. Also, make sure you're using the injector table and not the airflow adjust. Use the greddy software (not the tools) and check your injector duty cycles. Are you seeing normal values? Should be damn near 1% at idle. I have a feeling that something else is causing your problem, be it a vacuum leak, bad map sensor, etc.
How much reading have you done on the emanage? I know the manuals suck, but from your posts it looks like you need to do some more research. This forum http://diytuning.com/
has a much better emanage following and should have all the documentation you need.
Edit: More is coming back to me.
You also need an 02 clamp if you don't have one. PM or email olderguy on here for one. It's a simple circuit activated by a pressure switch that will tell the stock ecu it's seeing stoich when under boost. This will allow you to basically add on fuel to the stock ecu's tune (you'll have to add a good bit) without having to fight it.