It sounds as if you're pretty new to RPGs in general, is it true? After a game ask yourself and your players a question: did you have fun? If yes, than it was a good game, and you can only improve. RPGs (and 7th Sea 2ed in particular) are not like video games - a lot depends on player decisions, which can take your game to places you didn't anticipate. So don't overplan. 

You can find my session reports elsewhere on the forums - I started with The Caliberi Letters, then ran the Castle and since then my own adventures. 

Here are the links to the two sessions that Yaneky mentioned:

http://www.7thsea2e.com/port/forum/caliberi-letters

http://www.7thsea2e.com/port/forum/castle

Hail Inquisitor,

I've had some hit or miss sessions too.  Don't sweat it too much.  No one should be expecting perfection on your maiden voyage.

If it helps, I put together some "scenic battle consequences" long ago that are essentially random consequence generators for certain scenarios.  Basically, roll a d10 for each player at the beginning of the round and it gives him or her a consequence to deal with.  Some are better than others and I've only used them sparingly in my game.  At the risk of showboating, I do make use of my Risk Deck and find it makes Consequences and Opportunities much easier for me to visualize.  

Another thing that's been rattling around in my brain since I started watching John Wick run the game on Starter Kit is that maybe one way to present Consequences is GM vs Player agency.  So instead of giving the players a menu of options, the GM basically tells the players at the start of the Risk, "this is how the scene resolves itself." The players can then us their Raises to change those details and narrate what happens instead.  A bit more like the Houses of the Blooded mechanic, with raises acting as a sort of veto power in the scene.  I haven't actually tried this approach in play, so right now its just a thought.

Oh, and speaking of the Starter Kit adventure, I really like the "Notice roll" device John Wick uses.  Basically, the players make a Wits + [applied skill] roll and may spend raises to either ask a question of the GM, who answers honestly as best the Hero can see or know, OR to establish a FACT about the scene.  I can imagine this method could be extrapolated on in numerous ways. 

As far as Pacing goes, I've just pitched a lot of arbitrary dice rolls.  I set the scene, the players tell me what they want to do, and unless someone is directly standing in their way it works out.  

Another trick you can use, that isn't codified or explained in the core book, is what I call a "Narrative Sequence".  You can get a good look at it in Part 2 or the Quickstart Adventure.  Here is the relevant text:

"First, ask each player—one-by-one—to describe a dangerous situation from the previous months to show there was no help to be found in the Commonwealth or a short adventure that happened along the way to Vodacce. This situation should involve that player’s Hero making a mistake, stepping into danger, or helping out in a supporting role.

"Second, the person to that player’s right describes how his Hero saved the day. Perhaps one Hero rescued the other or one Hero overcame danger with his companion’s aid. Follow up each description with a quick Risk and encourage the players to narrate their daring escapes from the clutches of Duke Kazimierz and his allies. When players describe their dilemmas, assign appropriate Consequences for each Risk.

"Remember that the Hero who sets the scene is not the Hero who saves the day. The goal here is to bring the Heroes together, and to show that they have grown to rely on and trust one another in their journey. When setting a scene, if you feel a player puts their Hero in significant danger, displays a meaningful flaw or shortcoming, or otherwise does an exemplary job of showing another Hero to be awesome, offer them a Hero Point."

It's a lot like the Dramatic Interludes from Savage Worlds and I really wish some form of this had been included as a formal tool in the core rulebook.  I think its a great tool to help out with long term, zoomed out scenes.

As to the PvP BS, here's my long standing rule from my old teen roleplaying program: any physical attack on another player costs you a Hero Point.  I can see how this could be a tricky proposition in 7th Sea, but I think it would work out well in the end.  Players have enough control of the game that if the Pirate player spends a HP to push the ex-ATC out a window, that player could easily spend a HP for an awinging or a wagon full of straw to break his fall.  Ultimately, it becomes a zero-sum game that punishes the offender in the long term, and it doesn't take much in the way of basic math to figure that out.  I might tweak the rule just slightly so that the offender's spent HP goes immediately into the Danger Pool, especially if you are using the Khitai Peril rules.  That alone will do a lot more to establish order than Corruption.

So there you have it.  Without more info on your game, I would stress a very light touch when it comes to Risks.  For instance, when the duelist started a bar fight you went right to an Action Sequence.  That makes sense, except that probably ate up more time than necessary.  You could have just made it a standard Risk or a Dramatic Sequence.  The duelist hands over a HP and the pirate gets an extra 3 dice.  Done.  It's tricky, I know.  A lot of assumptions from traditional RPGs don't apply to 7th Sea, and it's not always clear which way to go.  

I hope some of this helps.