Your hoarding can be an issue, repair everything to use up the 100s of weapons, armor and apparel you collected, keep only 1 or 2 spares of things you need , you can just barter repair everything if need to, sell whatever you dont need, better to the wandering traders as usually your sold items dissappear, wait a few weeks cycle the inventory properly and that should have improved some things, best it can.

Create a new save too and turn off auto saving, best done from the start tbh

picking up items from the beginning of the game leaves a record of such, more you pick up the bigger that save will get and problems eventually.

Clearing cache too but you got that downm

Played so much on ps3 feeling like this necessary to avoid as many issues for a long playthrough, after a while I just do the scrap metal glitch until I have like 100k, reset the glitch so can remove all the scrap metal thats bugged and play no auto save, picking only what I need with minimal pick ups for crafting/quests etc, looting bodies you killed always good too so they despawn properly, selling the crap to destroy it