Okay I've just tried fixing with mods and I want to tell what happened just if it helps in any way fixing this problem (I was also wondering if it would help to share the save files? I don't really know how to do that)
Since the only save I had close to when i started playing with Cottage Living was already after a couple hours of playing, and I didn't want to revert to my April save, I had to deal with the empty households.
I went through all the townies in my "other household tab" and made the ones I wanted to save marked as played, and deleted the others, including the many empty households using MCCC , I also took off all of the Wild Foxes traits from lots . During that I already had installed bienchen's townieoverhaul mod the way explained by them in this forum and I also deleted the localthumbcache. After that I went back to my HoB sim (she lives in 5 Cobblebottom Street) and called the original HoB NPCs to reassign them as their village roles using Zero's mod. After that she went to sleep and I went through the day, everything seemed normal. The next day though, no one spawned in Finchwick (I talked about this happening before on this thread) and the lag started again, I went to the household manager and the empty households were all back and my save went from 97mb to 120mb, which i know it already bloated but like I said I had already started playing with Cottage Living and at that time I wasn't actually getting lag which is why I didn't catch the empty households sooner. It took maybe 20 minutes to save and I thought maybe I should put bienchen's mod directly in the mods folder instead of on a subfolder.
I did that and started playing again but I didn't even need to wait a whole day, middle of the day the only people that showed up to finchwick was Agnes Crumplebottom and a guy that was assigned pub owner, I asked Sara Scott to come over so i could assign her pub owner and she said she was coming but no one showed up, I also tried using MCCC to summon her and it didn't work even though it's a cheat. My sim got a call from a friend asking to join her to the flea market, I thought maybe in another neighborhood things could work so I got there and other sims spawned, I was even able to call Sara Scott (she was also weirdly assigned the pub owner even though previously a random guy was assigned) but then the lag came back and time stopped working, it stopped at 10:44am when she was interacting with her friend, I couldn't interact with anything and even going to build mode or opening the settings menu everything kept doing their idle animation like it's unpaused, after saving and going to manage households, there were again the empty households...
I'm really hoping this is an issue that can be solved and not an infected save that can't be helped, while I do have older saves I hate losing so much progress with a family I've been playing with for five years :/
(I hope I explained this well, sorry if something was worded weird, english is not my first language)