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Welcome to the world of Calibre. All of the above, are very valid, especially the backup, and loading in batches and cleaning as you go.
I'm doing pretty much the same thing you are, and I am loading my books in batches. Once a batch is loaded, I then individually go through each book to check and verify that the metadata is OK. Some books are better than others. You will get a feel for those you can skim over, and those you have to go so far as to open up the book to make sure you even have a right title.
As "theducks" said, 'patience grasshopper'. It's far better to nibble away at a smaller amount of books at a time than the '5K OMG' situation. Ask me how I know...
Take your time, in manageable batches, and make sure you have a backup of your library, and the books you have not loaded yet.
Once you've loaded a book into Calibre, and have the metadata correct, you can use the GUI to do extensive searches, so you don't have to worry about the Calibre library, other than to back it up. As you get familiar with Calibre, you will learn that the GUI is everything, and treat the data library as a 'black box'.
As you run into problems, and I'm sure you will, search the forums. There is a lot of information here, and if you can't find what you need, drop us a line, and someone will be sure to lend a hand.
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