How do you add the PPAs?
When I use sudo apt-add-repository ppa:mpstark/elementary-tweaks-daily and do a sudo apt-get update I'm able to install elementary-tweaks without any problems.
So maybe you're right and something is wrong with your installation file.
Did you check the SHA256 sum after downloading the iso?
According to ElementaryOS Installation docs you should do the following to verify the integrity of your file:
In this example the latest 64-bit eOS ISO has been used.
sha256sum elementaryos-0.3.2-stable-amd64.20151209.iso
The output should be:ee737ffa6bf33b742c5a7cee17aa26dec5ee3b573cbbc4b53cbe2a2513c9197a
If you still have the copy of the ISO you used to install eOS, you can check if the file is corrupt. If so, you have to download the ISO and install eOS again.
EDIT: The links you posted doesn't work for me either. So maybe you just have to correct these in your /etc/apt/sources.list or the corresponding file in /etc/apt/sources.list.d/....
To be sure, I would remove all the PPAs wich gave you a 404 error and add them with sudo add-apt-repository ppa:example-ppa/abc.