I don't know how the mod in question works, but you may be able to fix it by a console command: Open the console (the key below 'Esc') and type
player.RemoveFromFaction 1d3fd
This removes the player from the Enclave faction.
For a moment I hoped it could work, as it made sense, but I tried and it didn't work

I can still "press E to talk to Enclave Soldiers", the only way I can make them hostile is if I unload a FULL magazine on them (a couple of shots don't do the trick). Perhaps there's a console command to make a faction hostile? Any further suggestions?
@Showler: As for the traces of the previous mods, FOMM doesn't see it linked to the savegame at all, it was a theory of mine, perhaps the problem's elsewhere?