Hang on a second! You wrote at the beginning that
"The database is 353Gb." - 1 B (byte) is 8 bits, so that's about 40GB.
But your db is only 310 MB !!! (seeing that your document size is about half of it, I assume the other is stored keywords and index)
http://en.wikipedia.org/wiki/Giga_byte
So that makes the conversation completely different!!!
Kinook, please reread this thread, it really shouldn't take 8 hours to manipulate 5000 items database. As you mentioned, it might be the undo of Recycle Item thing ...