First off, it has been some time since I had a lower level Guardian. So, I will probably throw abilities in here that you do not yet have, oops :-)
The thing to understand about Guardian spec is it is priority based - not rotation based. You have already noticed that the cooldowns don't line up -that is the intent of the designers. Juggernaut has the same kinds of cooldowns on the same abilities, so to me they feel the same when not watching the graphics.
You will want to use Sundering Strike as often as possible - it generates focus and your ability to tank is directly associated to your focus. It generates good threat too.
Hilt Strike, even on bosses, is a great way to keep building that threat. Sure, you won't get a Pommel Strike on a boss, but the point is to get lots of hate.
Riposte _ANYTIME_ it lights up, unless you are in the middle of Master Strike. Riposte ignores the global cooldown, so it is free damage.
You will want to have Force Stasis talented so you can throw it on your target - boss or not - to generate focus and threat. It acts as a small, free DOT while you are going into another ability.
I will typically use Master Strike right after Force Stasis, for non bosses. Otherwise, I will use Master Strike when one of my higher priority abilities is not off cooldown.
Talent your Force Sweep so that it lowers the accuracy of your target, since you will probably be a mitigation tank in the long run. Lots of endurance for Guardians is okay, but since we can wear heavy armor that provides mitigation that Shadow's don't get.
For a glance at the future, my typical opener is
Saber Throw - builds focus Force Leap - builds focus Sundering Strike - builds focus (and talented to give two sunders) Force Sweep - (talented to give four sunders) Guardian Strike - lots of damage when 5 sunders is up Hilt Strike - to finish getting threat built up fast
Once I open the fight, I go into a priority system, with a goal to keep my focus above 6 but generate threat. The scheme is highest to lowest priority:
Riposte any time it is lit Sundering Strike Combat Focus Blade Storm - to keep up Blade Barrier which soaks some damage Hilt Strike Guardian Strike Force Sweep - to keep the accuracy debuff on the mob Master Strike (especially when boss is channeling long cast time item) Force Stasis Force Push Slash if focus 10+ Strike if focus less than 6
But even the, with the opener and priority scheme, some end game bosses require slightly different approaches. For example, I will not Force Leap Karagga since I need the maximum amount of room to slowly kite him.