Either the Practice tool is bugged or Zed is bugged
My runes were mana regen yellows, lethality reds and quints, and tier 2 cooldown blues. I had stormraiders surge.
This was my build I was testing

I was vs a
Bot at level 18 and a target dummy.
I had 3 infernal drakes and had 20ish AD from MF from Zed ult.
Here is the bug: I had more lethality and armor pen then MF had armor but my E and Q were doing incorrect damage.
Looking at my skill abilities damage in the tooltip, my E showed it would do slightly less than 450ish damage while my Q would deal over 550 if the target has 0 armor. On the dummy I would do more damage with my Q than my E with no cleaver stacks applied, this is normal.
On MF with 0 cleaver stacks and with this build my E was doing more damage than my Q. I did this multiple times on her and kep getting the same results of my Q dealing less damage than my E on MF.
I did this for over 5 minutes last night and lost sleep. I will test this again later tonight so 1 of 2 things is possible:
Practice tool is bugged or Zed Q is not dealing the full damage.
On the bright side I now know how his W works after 4 years.
is bugged