To make sure I understand correctly, in my case I would change:
SetEnemy LETrangerFaction NCRFactionNV 1 1
to
SetAlly LETrangerFaction NCRFactionNV 1 1
Is that right? Or do I change the numbers to zero? Also, just curious what type of mods you think might be causing the conflict in the first place? Thanks again, I appreciate the help.