So, its late game, and im at war with Cesears legion. I have a large army and im not suffering from anything, apart from resistance.

Its near IMPOSSIBLE to play this with resistance, as the NCR is so big that your smallish army, equipment and anything is going to be able to do NOTHING against the partisans when you take them over. It gets to the stage when EVERYTHING is in anarchy, and my army gets deleted, as attrition is 100%, meaning im defenceless, and CL marches over me like it was free. Although this is by far one of my favorite mods, its almost unwinnable, hell, UNPLAYABLE with resistance.