How can I Automate MongoDB schema design from existing MySQL Database and Logs?
I would not recommend doing automatic migrations from any relational databases (or other that differs in logic) to MongoDB. Of course it can be done, but the database performance might not be (and will most probably not be) good.

Now, answering your questions directly:

1) what do you mean by MySQL parameters?

2) Check the official docs page about the topic: Data Modeling in MongoDB

3) This question has already been answered in StackOverflow - Embed vs Reference. 
Nevertheless, here is where automatic migration rules will most probably fail. You need to decide this based on your use cases and necessities. Also, be aware that mongoDB doesn't support joins (meaning you will have to do it manually on the client side).

4) Only know MongoHub - it has an import/export tool that supports mysql