What I think should happen with armor penetration:

Make Black Cleaver, and then two primary armor pen items, Last Whisper and an item that is currently unnamed.

The unnamed item would build from brutalizer plus something else and give 15 penetration, make the armor pen from Brutalizer a unique passive called Piercing Strikes or something.

At level 13, and with like 1k more gold, so a total cost of about 3k gold, you can upgrade it to the final form which gives like 50 armor pen. This item is unique from Last Whisper so you choose between a shitton of flat pen to rape squishies or %pen to shred tanks.

The reason why it requires level 13 is that otherwise you'd rush it and destroy everything, which shouldn't happen.

Zed now has to choose between the more reliable LW or the ultimate squishy shredding power of this new item. Move some CDR elsewhere so that they still have options for 40%.

Also remove the armor pen from the jungle item and give it some more AD since it's the reason why the freelo junglers right now are Hec/Jarv/Vi.