I think fflogs would be good enough. The duration of fight plays a part in your final dps, because the longer the fight goes, the higher you can get, but you should be entering final phase around 940-970 (or higher if you have NIN/AST/MCH) and going up from there. If you're starting *significantly* lower than that, your issues are probably in earlier phases. If your dps drops from where you enter to where you end, you're messing up in final phase execution. The only times in final phase that you should be off the boss for longer than half a gcd:

1. Towers + Dragon Rage
2. Lightning Storm, if you get picked for tether or dive
3. Fire & Ice - you always wanna run off for this