When minimizing, not have new window of same app come to focus
Have you considered using CMD-H to hide the application instead of minimize it? If you minimize a window, the app that owns that window is still the focused app, but if you hide an application, it will change focus to the next app in the switcher. 

I can't help with the second part of your question. I assign apps to spaces so they don't clutter my spaces (even though they do sometimes - I'm looking at you, Photoshop).