I've recently 'fixed' it temporarily with a complete new install of Fallout 4, and modding the game again from scratch, but I'm simply just waiting for this issue to come back again.
I'm just not noticing what causes it, or even if any one mod does cause it or if it's a culmination of things. I've repeatedly started modding the game from scratch again and again, only to keep coming up with this issue. I run a pretty decent setup for a pc, which has no problems at all running any game yet, (sometimes even two at the same time). A lot of the time, the game just stops and gives me the loading screen vault-tec symbol in the bottom right while it loads up the open world I was walking into. After a short sprint (or even a jog) roads, buildings, objects and enemies fail to load even a little bit (I've fallen through bridges and roads before now only to get stuck when they loaded on me, or even load up in the middle of a pack of Super Mutants).
But after a while, while running from A to B in the open world, (not just in cities, but even in barren areas) things start loading slower and slower until it's almost unplayable without fast travelling. I set up my game + mods and start a fresh save, everything runs fine except minor issues barely worth mentioning. But I can't find a definitive answer or fix for it. Ok I've been googling and searching for a reason/fix for this issue for quite a while now.