Hi Artūras, and welcome!
I'm not sure why you would still want to use Flash at all anymore, when we can use HTML5, but here a few stabs at your questions about Scala.js.
There are 2 big parts in this file. The first part deals with translating everything that's "outside methods", i.e., classes, traits, implementation classes, fields, module accessors, and the method signatures. That part ends about here:
Further than this high-level view, the comments in the code should give a clear overview of how it works.
That's the basic idea, and to someone with the knowledge of the Scala compiler, a prototype that supports all-but-the-corner-cases can be implemented in a few months, possibly weeks. Then comes "all the rest": corner cases, tooling, integration with sbt and IDE, unit testing capabilities, testing of the compiler itself, libraries, optimizer, etc. This takes, well, years, and the support of a community, which I've been very lucky to get quite early for Scala.js.