When I play Zed I do very little damage with my abilites
Here are my runes
2 Quints AD 1 Quint AS 9 Marks Armor Pen 9 Seals Armor 9 Glyphs scaling mr
Masteries
Ferocity(6) Cunning(18) Resolve(6)
Fury Wanderer Recovery Double Edged Sword Asassin Tough Skin Merciless Dangerous Game Precision Storm Raiders Surge
I build the recommended items like duskblade botrk black cleaver yomuus etc.
press A then click the enemy champion/turret/minion etc.
YW
Your runes look good if you're still having trouble try switching to AD marks
Go 12-18 Ferocity: Fury Double Edged Sword Natural Talent Bounty Hunter Cunning: Wanderer Assassin Merciless Dangerous Game Precision Thunderlords Degree
Thunderlords instead of stormraiders will give you that extra burst and natural talent will give you that extra AD.
For items I usually go
for that armor pen first and build into 
and then the rest of the items depends on the enemy team and how far ahead I am.
If you are having trouble with their AP damage I'd build a 
Mash R and pray, like every other zed player. He just sort of does damage by existing and mashing buttons, just play more until you get his combos figured out completely.
Sounds to me like you are messing up the combo, you runes look fine, i however just use full AD and then the normal health or armor for defense.
Always go thunderlords.
For build, i like to rush a , rush the arm pen part first. After that, get either a duskblade, or a black cleaver depending on the enemy comp. Then go whatever you want. But your first 2 items are very crucial.
So your main combo, is W, E, Q to poke and harass throughout the laning phase, but when you get your Ult, what you want to do is R onto them and E, Auto attack, switch places with your clone, and then Q them, which with cdr, you will have your E again after your Q, so use that again.
In simpler terms, W to get a clone on the field, DO NOT swap places with your clone yet, it is your escape route. R, E, Auto, Swap places with clone, Q from a distance, and E again after it comes off cd.
This combo is not only safe, but effective, but it's downfall is it revolves around super quick muscle memory and CDR. It'll take a while to get used to the combo, but once you got it, you got it.
Again that is W, R, E, Auto, W, Q,E. That's the button sequence. OF course if they flash, you will have to mix it up a bit and maybe switch your E for your Q in the beginning/
The issue with Zed is, it's situational, if they have flash or dash, or a passive that will eat your thunderlords etc, you just gotta make sure to land enough to proc thunderlords for your ult.
Good luck!
