I'm going to try releasing my pack today in a few hours. It's already at 3,385 files now and folder size is just 340 mb :) Was testing it out last night with Kyler2's mod too and the body-image button does cause the game to freeze with how many files it's trying to load so would have to use the random portrait button feature instead to change your portraits + body images. I only tested this early game too so not sure how it'll act with many npcs, when many portraits are trying to be loaded.
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I've got a mod in the works for the portait/body buttons to load images on-demand when you scroll to them, instead of everything at once. Probably release it in it's semi-broken state as that's better than them not working at all on large collections. Basically, after loading, you need to scroll some once so it loads the first set.
It shouldn't have any impact late game. The most intensive point is when you first load a save, or start a new game. At that point, it re-populates all 3 slave traders, so generating 15 or so at once. Unless you mean something else? In general though, none of this behaves really any different late game vs. early, if it works fine with 3,385 now, it'll work fine with it end game too.