Without having run the numbers, I wouldn't suggest stacking these at all. I like to try and have a haste cooldown up at all times - this smooths out cobra shot, while at the same time increasing the chance of your RPPM trickets/gem proc'ing. It's quite possible at the moment, and with the T16 2p bonus meaning AS reduces RF's cooldown it'll be even more viable next patch.
RF would take priority, as the focus your pet gains from it can then be used more quickly as your pet still has the frenzy stacks.
I assume you're asking this question from a min-maxing perspective, in which case I honestly wouldn't listed to Trollsroyce, his Focus Fire usage seems more like a comfort thing of having a Haste buff always active rather than maximizing your damage through proper cooldown usage.
Rapid Fire is always stacked with other cooldowns. Your first and second Rapid Fire are used back to back at the start of the fight with all your other cooldowns and your third is used with Bestial Wrath if the fight is under ~5:30 or if the fight is over ~5:30 you'll hold your third rapid fire to be used back to back with your fourth with all cooldowns exactly like in your opener.
Focus Fire (assuming your gear is up to date with full RPPM items) should be used whenever it hits 5 stacks aside from during Bestial Wrath.
I always use FF together with my 2nd RF if possible so i can get another high chance for a trinket proc. Besides that i use RF or FF in front of cooldowns for the increased trinket proc chance and stack them together with the 2nd 5 minute cooldown burst.
If my rapid fire has like 5-10 seconds left I'll sometimes put focus fir on when it hits 5 stacks, just because I try and get as many stacks of frenzy during a fight as possible, only time I don't activate focus fire is when bw is up and when rapid fire was just activated.
I assume you're asking this question from a min-maxing perspective, in which case I honestly wouldn't listed to Trollsroyce, his Focus Fire usage seems more like a comfort thing of having a Haste buff always active rather than maximizing your damage through proper cooldown usage
You may get higher burst, but I guarantee that my sustained damage would top yours.
At the end of the day OP, do whatever feels most comfortable to you and your playstyle. Some people like to pop all their CDs at once to reduce ability bloat (you could even macro FF and RF together if you want to, as RF is not on the GCD) and that's fine because that person will probably do more damage that way than trying to string them together or use them at precisely the right time.
Chances are, if you wait to use one of these CDs, it'll be highly likely that the damage you'll lose waiting for the right time will be higher than the damage you gain for popping it at precisely the right moment. Obviously you want to tailor these in certain fights to line up with raid damage buffs (banner etc.) or with encounter damage buffs (Jin'Rokh puddles).
Do whatever feels most comfortable to you, and you'll be maximising your personal dps
Glurp is actually correct on this. Granted, I find myself holding onto Focus Fire during Haste effects just because being under GCD cap firing .7 second Cobras throws me off and feels incredibly choppy.
I've stacked RF and FF several times, that's just how the cards fell, and wondered if I was doing it wrong (the meter said no, but a LFR meter isn't telling me a whole lot anyway), so I'm glad to see it isn't a "huntard" move (even though I hate the word).