MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Let me try to answer all your questions.
First off the .skp file is the sketchup document. It is the cad drawing of all the components so if you wanted to edit or modify anything you would do that with sketchup
Second, the printed case only fits the Hero1 and 2. I am working on a Hero 3 case but it is on the back burner for the moment. You could however stick the Hero 3's waterproof case directly to that flat plate for the time being. It will be a little heavier but better protected from a crash.
Third, that is a touch question to answer. It all depends on your controller, how well you balance the cg and the props and motors and how well you fly it. The quad can be made to fly very stable with just a KK board but it takes a fair bit more hand flying than say a NAZA or a APM. The KK is a good inexpensive place to start though. It can fly as high as you can see or even higher if you have a fpv system on it. I have flown my quad about a mile and a half away with a UHF system on it.
Hope that helps, if you have any more questions feel free to ask.