The only way I know of to get modded items working mid-playthrough is by changing the meta.lsb of the unmodded savegame to the meta.lsb of a modded (new) savegame, tricking the game into thinking that the mod is actually enabled.
His problem is different though, as he's overwriting stuff in Data\Public\Main, which is the Main module and is always loaded. The problem is - I think - that both mods try to overwrite the same file in RootTemplates
... this is why just changing stuff in Mods\Main\ or Public\Main\ instead of setting up override .lsx-es for the changed root templates only is a very bad idea (and its only getting worse as more and more mods pop up)
