You should clean the official DLC's. Particularly Knights of the Nine. It has hundreds of duplicate edits.
When your cleaning, be sure to remove identical to master edits, undelete and remove references, and sort masters and clean masters.
@OP Yes.
I did this (except the last part).
Over the period of a week of doing nothing but working on getting Oblivion mods installed and working (FCOM + numerous others) I found the biggest thing to help my game being stable was doing the TES4Edit cleaning. It would really make much more sense for people to do this before uploading and even having a certification program where TESNexus or whoever ensures each mod hosted is pre-cleaned then given the tick or something.
Other than that it was a matter of using http://www.tesnexus.com/downloads/file.php?id=21862 on missing meshes and hunting down where I'd gone wrong in installing. Or even updating older mods to be more compatible. (I recall editing the paths in Slof's Robe Trader.esp to be up to date.)
For someone new to the modding scene the early recommendations appear to be OBMM but after a few days it becomes clear WyreBash is required for the larger combination of mods so now I use a mix of both. (Primarily using WyreBash.) Also took me a while to figure out the best archive invalidation method is the "ArchiveInvalidationInvalidated!.bsa". There is way too many old sources referring to BSA redirection etc.