Well, I was bored and tried to recreate the Rune Page and Masteries of Stonewall's Kha'zix jungle, and what I got was pretty messed up. 3 AD Quints, 3 AS Reds, 6 AD Reds, 6 AD Yellows, 3 Armor Yellows, then 9 Armor Blues. Masteries made no sense, since Stonewall neglected to put stats into Defense and Utility, so unless he put points into Crit bonus... either way I inserted defense points. This was to match his level 1 stats perfectly (though putting points into Defense made mine higher in that aspect).
This was me being less crazy and more curious into how he got his times (which was 15 seconds faster than my AD/Armor Pen set-up). This also uses only 4 sets of runes, instead of 6. I'm wondering if there's a less convoluted set-up for equal or better results. Also if he has armor pen from Runes and maximized them better, I wouldn't know (don't think it's possible.
Edit: I tried a different set-up, one that gives 9% CDR (instead of 1%) and 4 more armor pen at the cost of 3 AD and 7% AS, which I think is a little better for optimation of your Kit. There's alot of different options, but Kha'zix looks to have 3:40-3:43 as his best lvl 4 clear without a leash.