I'm hardly the most experienced, but here's what I'm starting to do. I like to break down the stakes into External, Internal, and Philosophical (this is a tool I've appropriated from Michael Arndt). That last one, for me, is the guiding rule, theme, w/e, that helps me make decisions and brainstorm new complications. Then, I look to see if each of those stakes seem lost, impossible to overcome at the climax. Knowing the stakes also let's me choose the right ending to build towards. In parallel, I draw Dan Harmon's story circle and make sure each of the eight points (You, Need, Go, Search, Find, Take, Return, Changed) is represented in the story. And of course, I look at it through your lens of characters' narrative functions. Hopefully this helps me identify what I feel is lacking :)

I stumbled upon a free rewrite workshop(via conference call) through Screenwriting U. It was 2 hours long, of which I expected about half of that to be a sales pitch for their online classes. This was not the case at ALL. It was a super helpful lecture. I think it's offered several times a year on a first come, first served basis. A handout is included, still using it months later. http://www.screenwritingu.com/

Just looked it up....there's one coming up in January. http://www.screenwritingu.com/rewrite_conference2.html

I just listened to an old podcast (2008) with Christopher McQuarrie. I liked what he said when asked about empathy for the protagonist. He said he doesn't give a shit about empathy. He and Tom Cruise (while working on Valkyrie) on wanted two things: Clarity and Location. Clarity and Location. An interesting approach. I'm going to give it a shot.

Hardest thing for me is to lose those nice, funny or otherwise beautiful bits that have absolutely nothing to do with the theme of the script. So I keep asking myself what´s essential? What´s tightly tied up to the story? And what raises the stakes even more?

I agree with Scott that 90% of the time it's related to character. If your character knows what he wants and knows the world he inhabits, the rest can generally take care of itself. One of the issues I face is overplotting. I would say to look at your script and see if it's too intricate for its own good. If so, take some of that energy and retrain it on your characters.

I tend to get caught up in working the plot to it's fullest extent, and forget to work the characters to breaking point too. So for me, it's a question of going back and making sure that all those exciting plot moments have a real impact on the characters, and that their emotions, status and desires change from scene to scene.

Michael Arndt's talk on this subject at AFF was fantastic. I do the External/Internal/Philosophical breakdown too.

what did he mean by that?

If you can find the interview with him and Jeff Goldsmith, it might make more sense in context. He was talking about rewrites on Valkyrie. Goldsmith asked him what they did to create sympathy in the first five pages. That's when he said, "I have a big problem with the word sympathy." He then explained that Tom Cruise only cares about: "What's happening in the scene? Where am I in the movie?" If the audience understands those two things, you're solid. (According to them at least.) McQuarrie then added, "I just need to know why the character makes the choices they make. I don't need the audience to identify or feel imbued by that."

So by location, I guess what he means is "at what point of the characters journey are we?". That makes sense.

I try to focus on Tension. Tension creates drama and excitement in your story. Characters should never get anything easy or have things just handed to them, not even a glass of water. They should have to work their ass off for everything. Then when they finally get what they want in the end the audience will feel they earned it...

Tony, David Seidler (The King's Speech) said much the same thing in an interview I did with him recently: Find the thematic center of the story, then everything you write has to be tied to and advance that. Anything that doesn't, you have to omit.

A lot of great suggestions in this thread, thanks. Two further points: * This point about overplotting vs. under-character [poor description, but you get my point] is noteworthy. Not to say plotting isn't important, of course it is. But having read way too many scripts where the writer hits all the beats just fine, but there's no real life to it, primarily due to a lack of depth re the characters, I certainly think it's critical to devote as much or more time with characters than with plot. As I noted in the OP, they are your story's lifeblood, heart and soul. I know for a fact spec scripts have sold and certainly writers have gotten repped where the story wasn't stellar on the plotting front, but the characters and emotional life of the story was great. At the end of the day, a script reader wants to FEEL something when they crack open a manuscript. Of course in an ideal world, the work you do on characters INFORMS the plotting process, there should be a synergy between the two. Again as noted in the OP, a story universe is comprised of two realms or aspects: Plotline (Ext World) and Themeline (Int World). A writer MUST do due diligence per the latter to craft a vibrant, alive script. * Earl's point about tension is spot on and perhaps the easiest way to do this is by making sure you've provided enough Complications, Roadblocks and Reversals. Create obstacles all along the way. If you need any paradigms for this, just watch any of the Toy Story movies as Pixar are the masters of this. This is not an easy instinct to develop because so much of our attention is directed toward getting the damn script done. So we have this constant forward momentum at work pushing us from Point A to Point Z. But we have to be willing to set that aside and muck up the Plotline by creating obstacles. Earl's point is so true: We want the Protagonist to "work their ass off" to achieve their goal because it makes the achievement of it that much more meaningful. Another talisman per this point: Watch the ending of The Silence of the Lambs. If the goal is for Clarice to shoot Buffalo Bill, the filmmakers could have just as easily had her blow him away in the kitchen. End of story. Instead he escapes into the bowels of his home and Clarice is forced to go deeper and deeper into 'hell' to find him [count how many doors / thresholds she has to cross, each one loaded with fear because you just don't know what's behind it]. So yes, make the way hard for your Protagonist. It will be worth it in the end.

Structurally, this is the main rewrite issue I deal with. (Dialogue is my other big thing). In TV, especially in pilots, this is a key consideration. When I'm rewriting mine, the key question that keeps coming up is: Have I revealed too much or too little about this character or, more commonly, the relationship between these characters, at this point in time, and how are events modifying the underlying relationship? Because TV shows, even more so than movies, are about character and the journey is about the revelation of character, over the course of a season or more. You don't want to give away too much, early on, but you also need to reveal enough to keep the audience engaged. You also need to give a hint/tease as to where things are going. It's a delicate balance, to be sure.

Thanks so much for answering my question Scott... and thanks to all the commenters for their input!!