I re-installed the game and with mods, there will definitely be silent crashes.

So I went to TES5EDIT, did it four times (Skyrim and Update), (Skyrim, Update and Dawnguard), (Skyrim, Update and Hearthfires) and (Skyrim, Update and Dragonborn). All of them I selected apply filter for cleaning, remove identical to master records and undelete references.

I then used LOOT to ensure correct load order.

After that, I ran with admin skseloader.exe and as soon as I used the console for coc whiterunbreezehome it just crashed. What went wrong?

P.S. It actually works now. I just need to fast travel somewhere else and interact with a few NPCs. However, I'm afraid that this problem would appear again? What could be the apparent cause of this and if so how do I solve it thanks.