The short answer is, it depends. If you're only comparing numerical data, there won't be any conflicts. In the real world, it gets messy. Collation depends on whether you specified binary or Windows collation during setup and on whether you use Unicode.
I googled <"sql server" collation> and got several useful links, many from MSDN.
To try to answer your questions:
1) You can specify a different collation for each DB and even for specific columns. The system is built to handle diverse collations, although the default is to be homogeneous. If you can keep the results straight, then use multiple collations.
2) Again, the system is built for multiple collations. As long as both instances have the proper language interpretation skills, you should be okay.
3) System collation is internal and may be irrelevant.
4) I see you've gotten an answer for this on another forum.