well it's good to know that other people have played much longer and don't have issues. I myself have about 4400 hours total played but my savegames have mostly been around the 50 day mark. I have used FO4 to make videos for the past 3 years using various mods for the video process. Whenever I finished a video I would return to one of my 50 day saves and start a new video using different mods. Some of these mods were new equipment, new face models, new lands, etc.
Some mods were probably more on the beta side and should have taken more time to mature before being released. But I think that's something that everyone that uses mods has to beware of. I suspect it does have to do something with one of these sketchy mods.
Then of course next-gen came along and who knows how that may have interacted with some of the mods. Now I have to figure out who is the culprit mod and whether removing it may fix the problem or if it's irrecoverable.