I'm not sure what magnitude of difference you expect from changing the order of JAs, you might be disappointed by the outcome.
Regardless this is what I prefer to do, which might not be the best but usually provided the best results for me.
A--------------------B-------------C
A: Starting point, 0:00
B: Impetus is over, 3:00
C: End of the cycle, 5:00
I use Impetus and Focus on A.
Focus is for two reasons:
1) The acc is gonna help build stacks faster
2) The Crit from Focus is gonna help compensate for the fact that my Crit+ Impetus stack will be low at start (they build up with each hit after all)
First point most of the time doesn't matter because I tend to cap my acc on targets regardless of my JAs. In some circumstances it's useful I guess.
When I get to B I use Berserk (often with Warcry too) and usually I go with Footwork as well.
I use Tornado somewhere around 1500 TP until Footwork is over, then I use Vsmite or Howling according to my buffs and the target until I get to C.
C is the end of a cycle and the beginning of another one. From the second cycle onwards I'm gonna be at A with ~1 min left of Berserk. This is gonna help with Impetus because for the first seconds my attack bonus from Impetus will be low (that too builds up with stacks)
Now to be completely honest I can't really make use of this cycle everytime, it depends on the content. Sometimes you're gonna have to spend time waiting for targets, for buffs, moving and whatever else. When this happens it can create hiccups in the cycle of course.
But in other circumstances it works well and so far it's what has provided the best results for me in terms of DPS output.
Small differences though.