With a tree of that size, you might consider sync-ing without your added media first.
Places don't seem to be a problem. I have read that PDFs can sometimes be an issue for sync-ing the media - not all PDFS, but a possible corrupt file.
My tree is a little over 10,000, with a great deal of media, and I rarely have issues.
If Russ is around the board today, he usually has the best advice.