You'll need to load up your mod in FO3Edit and delete all the records
from your mod that overwrite the vanilla trees. This will restore your trees to their original locations. Then you will want to move them again in the Geck and then generate a new LOD. The 'ghosts' as you call them are the LOD trees - the visual representation of the trees at longer distances. LOD data will remain even if you move the trees. I am guessing that by disabling them, the LOD Data has some null pointers (pointing to trees that aren't there) and this is causing the CTDs. I can't give you a how to on generating LOD data, I just know it takes a very long time.