Some thoughts....
Typically one does not want to store pieces of tightly interrelated information in different systems. The chances of things getting out of sync is significant and now instead of one problem on your hands you have two. One thing you can do with Mongo though is use it to pipeline your data in or data out. My preference is to keep everything in PostgreSQL to the extent this is possible. However, I would note that doing so really requires expert knowledge of PostgreSQL programming and is not for shops unwilling to dedicate to using advanced features. I see a somewhat different set of options than you do. Since my preference is not something I see listed I will give it to you.
You can probably separate your metadata into common data, data required for classes, and document data. In this regard you would have a general catalog table with the basic common information plus one table per class. In this table you would have an hstore, json, or xml field which would store the rest of the data along with columns where you are storing data that must be constrained significantly. This would reduce what you need to put in these tables per class, but would allow you to leverage constraints however you like. The three options have different issues and are worth considering separately:
hstore is relatively limited but also used by a lot of people. It isn't extremely new but it only is a key/value store, and is incapable of nested data structures, unlike json and xml.
json is quite new and doesn't really do a lot right now. This doesn't mean you can't do a lot with it, but you aren't going to do a lot out of the box. If you do you can expect to do a significant amount of programming, probably in plv8js or, if you want to stick with older environments, plperlu or plpython. json is better supported in 9.3 though at least in current development snapshots, so when that version is released things will get better.
xml is the best supported of the three, with the most features, and the longest support history. Then again, it is XML.....
However if you do decide to go with Mongo and PostgreSQL together, note that PostgreSQL supports 2 phase commit meaning you can run the write operations, then issue PREPARE TRANSACTION and if this succeeds do your atomic writes in Mongo. If that succeeds you can then COMMIT in PostgreSQL.
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
Best Answer
16 MB is the maximum size of single document, e.g. one user.
The size of the collection is limit by maximum database only.
https://docs.mongodb.com/manual/reference/limits/
So logging to the database should be no problem. In my opinion using sensible indizes including _id is superior to a heap of collections.
It is not clear to me what you actually want to store in your database so I cannot really comment on the structure. Generally speaking there are three ways to handle relations: Using arrays
If you give more details, chances are somebody can give you a more detailed answer.