Amor Pen and Armor reduction are different values. Dont get a last whisper and a black cleaver if you're gunning for armor because it goes reduction THEN pen. So in actuality you would be reducing his armor by 60 and then 40 x .4 = 16 armor. Brutalizer Black Cleaver and Starks are the only items with armor reduction. Nassus Rammus and Corki have skills to do so as well.
TLDR: You should likely switch last whisper to a zeal or a starks for movespeed or actual armor reduction.
So wait what you are saying is Armor Penetration is a "rating" where the more you have the more percentage of armor you ignore?
Here's a few examples:
1) The enemy has 100 armor. I have 60 armor reduction due to the Cleaver's debuffs, Last Whisper, and 15 armor penetration from runes. Reduction takes their armor down to 40. Last Whisper reduces that to 24. Armor penetration takes it to a final value of 9.
2) The enemy has 100 armor. I don't buy the Black Cleaver, but instead have a Brutalizer (15 penetration), Last Whisper, and 15 penetration from runes. Last Whisper applies first, reducing his armor to 60. Then my 30 total armor penetration takes it down to 30. See how Last Whisper was worth 40 penetration this time, but only 16 when paired with the Black Cleaver?
3) The enemy has 50 armor. I have Black Cleaver, Last Whisper, and 15 armor penetration from runes. The Black Cleaver does 60 armor reduction, reducing their armor to -10. Last Whisper and my runes do nothing because they can't take armor below zero. If I sell Last Whisper and buy Stark's Fervor instead, though, I can get their armor down to -35.
The moral of the story is that combining armor reduction effects with Last Whisper isn't very cost-effective. You want to either combine Last Whisper with armor PENETRATION, or stack armor reduction by itself without Last Whisper, maybe with some flat penetration on top of it if you don't expect the reduction to take them to zero or below. Magic reduction/penetration/Void Staff work exactly the same, by the way.