I just changed over to the kde4 version when ubuntu upgraded to 8.10, and have a high volume of torrents. They imported/work ok, but on startup I get hundreds of notifications that I am already downloading XXXX. I see no way to turn off that in the configure notifications settings. How to fix? Thanks.

Currently there is no way to fix this, you just have to cancel the popups.

There are about 4 thousand of them every time I start ktorrent. This makes it completely unusable. How do I find where the offending torrents are and delete them?

cd ~/.kde/share/apps/ktorrent
fdupes . -r -d -N;for f in *
do [[ -e "$f"/file_map ]] || rm -r "$f";done

Or simply next time you doesn't have any active torrents do:
# rm -rf /your_ktorrent/tmp_folder/*