Smallhagrid,
I would suggest trying to add and convert books in vastly smaller quantities.
As DoctorOhh mentions, your Add Books process was not optimal. There are a number of possible reasons, but most likely you have "Use Metadata From Ebook" checked (probably misnamed here, but the option is similarly named in Preferences>Adding Books, I believe) which caused some metadata to be added from internal, hidden sources in the ebook file itself and not from the file name.
Secondly, if
all of your ebooks don't follow an
exact file naming scheme, then you will also have problems adding books based on the file name.
Take a look at my message in this topic:
Tyrranasaurus Regex. Ignore all the Regex (or anything else that seems too technical), just look at the required format and read the warnings about how the import/adding process can be broken. Why is this relevant? Because if your filenames don't follow one exact scheme, adding them will result in a mess. For every naming scheme used, you would need a separate import regex. Your computer OS doesn't know what portion is a title, author or series. All it knows is the individual character string that makes up the unique file name. Calibre is slightly more intelligent, but only as good as the regex used to add books.
Remember also not to store your calibre library into the same folder as your original ebook source library. Calibre is going to make a single copy of each book in whatever folder you designate. But if you point it to your old library, you're going to have a library inside a library. (I don't think you did this, just figured I would mention it - just in case.)
At this point, your best bet might be to delete the entire messed-up calibre library and start all over again. Just make sure you didn't put a library in a library (as mentioned above) before deleting things or you might delete your original ebook files.