It's important to realize that the warp stabilizer cannot fix every shot. If you are planning very long takes with moving cameras then you have to either figure out how to move the camera smoothly or put things in your shot that will hide cuts and cover mistakes. Alfred Hitchcock was a master of this. There's a shot in Frenzy that starts wide over a public market scene, follows an actor through the street, continues with him inside a building, up a flight of stairs to a landing then up into a hallway, down the hallway to a door. The actor goes through the door and it rises revealing the scene inside through the keyhole. The whole thing looks like one continuous shot and it really builds tension in the story, but in reality it was five or six shots cleverly cut together to hide the transitions. An example of careful planning is one of the first SteadyCam shots in a feature film. In "Bound for Glory there's this very high wide shot of the migrant workers camp and the camera slowly descends to the ground then follows 'Woody Guthrie through the crowd all the way to front of the group where the farm workers are waiting to be called to work. In this case it was a single shot carefully choreographed where Garret Brown (perfecter of the SteadyCam) was way above the crowd in a bucket and as it was lowered to the ground he stepped out and followed the actor through a carefully stages and rehearsed path to the conclusion of the shot. What both shots have in common is careful planning and the right equipment. It sounds like you're stuck with some footage that was grabbed without much thought or care and now you're trying to fix it in post.
In your case, where there are things in the scene that foul up stabilizing you need to cut the shot. Some shots just won't stabilize with the tools in AE. Some won't stabilize with any tools. Stabilize what you can, then try and piece the parts together. Think first about telling the story effectively. Think secondly about impressing someone with your fix it in post skills.
Nobody is amazed any more by a long smooth moving camera shot so unless it's really necessary to tell the story don't fret about cutting it up. Sorry, there's not much more that you can do. When it's critical to telling a story to have a very long moving camera shot then you have to plan for it. In most cases, your story, and your film will be better if you cut things up.
As Rick said, you are looking for the magic button that doesn't exist. Warp Stabilizer may be able to fix many things, but it's inherent in how it works that it won't be able to fix just as many things. Anything that erratically disturbs its underlying vector field calculations is just guaranteed to throw it off and whether that is a dust flake swirling around close to the lens or someone walking the corridor is the same. In the end you have to realize you probably shot it the wrong way and it may not be possible to fix it in post in any way at all. This is stypical steadycam stuff or even something for a rail dolly....
Rick, your response was based on a false assumption. I re-read my posting and thought I'd made it evident that this is NOT (repeat NOT) a travelling shot. To be more precise, it is a lengthy shot of a stage from a fixed perspective. The camera never even zooms. A string of 24 or so light bulbs overhead forms an extremely distinctive pattern, not just all in a row but rather like an inverted '3' if you were to connect the dots, and each bulb is separated by a gap of a foot or more.
Apart from the fact that my handheld camera is bumpy, my perspective on the scene is static. That said, I'm shooting from a low angle, so on occasion, someone on the stage briefly obscures my camera's view of, at most, three of the bulbs. So as not to confuse Warp Stabilizer, I made a mask that blots out ALL stage action yet reveals the light strings at all times.
I put out there two queries, but in fact I have since found my own solution to the first: I output the isolatred light sring to a new video file.
Now my only problem is how to apply the Warp Stabilizer's work on the shot with the light string (isolated of all distractions) to the shot it derives from.