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.
