A couple of things:
If you have a vacuum secondary Holley, you won't be able to see the secondaries open - they only open when the engine is under a load. You CAN watch the secondaries open with a double pumper.
Disconnect the linkage at the carb and manually open the carb as far as it will go and make a note of where it stops. Hook the linkage back up to the carb and have a helper mat the pedal and compare. If it doesn't seem to be going all of the way, do a couple of things:
Disconnect the linkage from the carb (again) and pull the rod toward the front of the engine as far as it will go. The lever coming up from the firewall will hit the back of the intake manifold. Hold it in that position and thread your little rod to carb connector doohickey until it lines up with the hole in the carb linkage, and re-attach the clip.This should give you max travel distance with your set-up. Also, as stated earlier, make sure the pinch bolt/nut is tight where the throttle lever joins the pedal assembly at the firewall. You can get a fair amount of slop there.
I had the EXACT same problem as you, and no matter which hole I used on the carb, I couldn't get WOT. What I finally did was remove the gas pedal assembly an heat it and bend it so I could get more travel. It in effect makes the gas pedal sit a bit higher up off the floor. A pain, but works perfectly now.
Here's a picture of mine - I made my own rod to the carb. Disregard the kickdown on mine - it's a TV cable for an overdrive automatic - not the same as yours.
Once you get your throttle squared away, then you can reset your kickdown cable. Get under the hood and pry up the plastick locking clip on the kickdown cable. Open the throttle to WOT, and, holding it there, lock the clip back down. Release the throttle, and you're done. Good luck!