Pantsu

There are several tutorials online. To edit a ROM, you need to extract the files first. As far as i am concerned, there are several tools online that help you with that. After you extracted the ROM, you will have all the files in a folder, chose that folder with PK3DS and you can make edits as you wish. After that, you just need to rebuild the .3ds as file if you want to use it.

Yea, i scrolled up a bit and realized it's been asked a lot of times. Also, i think i have made kind of a mistake, i intepreted "Pickup Items" (in pk3ds) as overworld items you can pick up, but judging by the layout it's about the ability "Pickup", thus not changing anything about the Overworld items. And then going by what i read, Overworld item manip would change something with scrips, which isn't really doable, so i assume it's impossible at this time to randomize the items you pick up in the overworld with pk3ds? And sorry for not looking all that up before replying, would've been a better move.

Seems to be a common issue from what i've read up. I have the same issue and sadly no idea how to fix it