Opening rotation is key. You want to pump out the most damage in that first few seconds while you have all your procs up. The way I do mine is: (Battle Stance) charge> Skull Banner > BT > Avatar/Bloodbath > Dragon Roar > Reck if 0 RB stacks > CS+IR > Reck if 1+ RB stacks > BT...
The reason I check to see my RB stacks before I hit reck is because you don't want to overproc by getting a CS crit and a BT crit when you've already got one stack. BT during reck is guaranteed to proc RB so you don't have to worry about it being unusable.
Another good habit to get into is pre planning your encounters. Look at previous kill times, guilds similar to your's kill times and figure out how many times you're going to be able to use your CDs. For example, my elegon kill is going to be around 9:20-9:45 so that means that reck can only be used twice so you should use it in the beginning then save it for execute phase, avatar can potentially be used 3 times but around the 3 minute mark you're generally on conduit/add phase so it might be a waste but you have to be the judge. Last use should be saved for reck. Continue doing this for all of your offensive and defensive CDs and tailor them around certain aspects of each fight and you'll notice a substantial dps increase.
Quick things to look for would include burn phases, increases boss damage taken phases, saving defensive CDs for points of massive raid damage, etc.
One thing that a lot of people overlook is stance dancing. Yes, it's still alive and well in MoP! Whenever you're in a period of sustained aoe damage or whenever you know you're about to take a decent size chunk of damage, preemptively hope into berserker stance and use it to your advantage. Same applies to defensive stance when you know that the incoming damageight possibly kill you. Just be wary of your threat while in defensive and get out of that stance as soon as you can.
Ill add more and go over your logs later when I get home.
Hope this helped