Your question has led me to do a number of different calculations on FemaleDwarf. While logically we should be able to define either KC or KS as the priority choice between the 2, no matter how I move them about (while maintaining the rets of the relative priority) I see 0 change in dps between KC>KS and KS>KC - even when switching around BW so its in between KS and KC (KS>BW>KC), so simulations show that it doesn't matter.
Now for the practical and logical approach;
Using the results from a t13 normal equipped raider (all 5 tier pieces), Femaledwarf reports that I have 35,284 effective RAP on my target. KC damage is (849 + 51.6%RAP) * Mastery. KS is 150% weapondamage + 543 + 45%RAP so the differences between the 2 is (excluding mastery) 303 + 6.6%RAP in favor of KC versus 150% weapondamage.
For a weapon like
[Vishanka, Jaws of the Earth] the weapon damage is 2629.76 + RAP/14*2.8 or 20%RAP. It then becomes 303 + 6.6%RAP versus 2629.76 + 20%RAP, or in other words Kill shot is the clear winner here.
Now the thing that is most likely playing in to even it out so completely is the differing cooldowns, and what you replace. If you prioritize KC>KS then KS is still fired as often as possible (more or less) by pushing out Arcane Shots (though in reality it pushes out Cobra Shots, which are even lower on the damage chain, since we don't need to use CoS to gain focus we haven't used), while if we prioritize KS>KC then we push KC by 2 seconds, or a third of the CD, thus costing us 1 full KC every 3rd time we do so, or in sim terms, costing us a third of a KC.
That 1/3*KC is more or less exactly the gain of KS>KC - which is the reasoning I used orignally to prioritise KC>KS.
In summation to that, you can do it either way, its more or les a wash theoretically speaking, though I will retain the KC>KS priority, as that will, in practice, more likely allow more of both and pushes CoS instead of KC, allowing more instants.
Also, while doing these iterations I have looked at the relative values of secondary stats, and can confirm that, regardless of the projected values (I'm looking at haste specifically) the priority is
Hit (to cap) >> Crit > Mastery >> Haste
Even while the tool is valuing haste higher than crit and mastery, and mastery at the bottom, reforging haste to mastery on a single item at a time consistently provides a dps increase. This, of course, goes very nicely with the priority, as we are pushing the only casttime shot we use (CoS) to the very bottom at all times, and with 2t13, we will use it even less, thus gaining almost no value from haste apart from the autoshot increase.