I added 40,000+ files and it took quite a while. It has also taken quite a while to sort through them and find the best copies etc as I had a fair amount of duplication.
My advice is to name/rename the books in Calibre to the original published title.
I had started out renaming all my books to include author and series in the file name and had to redo all of these in order to get metadata etc.
As to pdf's some older ones do not display correctly in newer versions of adobe reader and vice versa. They can usually be converted or fixed but not always worth the effort.
I did the brute force method, adding them all at once with merge the filenames checked then went through author by author downloading covers and metatdata and using a custom field to note problems with formatting etc. When I am finished with this I will then fix whatever ones I can which should be most
In many cases Calibre got the correct title and author from the metadata stored in the file.
There are lots of threads with regex's that will corectly deduce the correct author title from a group of similarly named files. I stumbled across them too late and am glad as I would probably still be importing instead of almost done with the organizational part.
It is a lot of work, but eventually you will end up with a nicely organized library and you can export your books in pretty well any way you want when this is done.
Helen