I don't have the software handy so I can't answer some of your questions, but the whole thing seemed extremely dumbed down to me. For example, on intake manifolds if you wanted to test a sheet metal manifold, you had one selection. With the Performance Trends software, you can vary the runner length, runner diameter, and taper of the runner, plus the plenum volume, to see what the effects would be on the horsepower curve.
The software I'm using was purchased quite a while ago, around 2006 I believe. I'm sure there are more current versions available than what I have, but unless they've made radical improvements to the Dynomation software it just doesn't measure up. By the way, according to a Ford engineer I know who works on their boosted engine projects, Ford uses the Performance Trends software.