Fallout NV is crashtastic, no matter what you do, and even just the vanilla version without mods. But even then, you'll never be completely rid of crashes with it. I am new to the whole Fallout game series and so Fallout4 is my first and I love it so I bought Fallout NV when Steam had it for sale with all the DLC included. But I find it very hard to sacrifice any of them now. I've been trying to do the exact same process to fix my own crashes and I can't make head nor tails of what the problem is. If this were the case you'd get crashes no matter what mods you had active, so disabling them all and making sure there's no garbage in your /Data folder would be a good first step. Followed your steps and disabling everything and then deleting the remaining folders. Launch Fallout 4 and load a few games just to make sure it isn't crashing.
