Basically the issues that you are having are purely to do with tuning of these sub systems. The idle PID looks a little bit too neat for my liking, and using someone elses setup is okay, if you're happy with their level of tuning, they might not mind a bit of oscilation after startup.
What you might like to try is to turn on every high current electrical item in your car and see how the PID tuning copes with it, I'd bet that there will be some oscillation as the IACV is opened to raise revs in order to counter the load on the engine.
Datalog the experiments and we can look at the oscilations in the RPM, also datalog the boost issue, there are many people who can advise when the data is available.