Conflict, Plot Holes and Loose Ends: All in a Day's Work!

I read with interest 'Don't Lose the Plot' in August's Writing Magazine. Lorena Goldsmith's article outlined many difficulties writers face when developing their manuscript from a basic outline to the fully formed manuscript.
Within the article, Lorena writes about weak conflicts and contrivance, two issues I am struggling with in my latest children's novel - my prequel to Driftwood and Amethyst, currently known as Before Driftwood (working title).
I, too, am constantly striving to ensure that the conflicts faced by my two main characters, Holly and Ethan, are believable and uncontrived - within the story's universe of course. I so hate it in novels when a character  suddenly stumbles upon a hidden trap door or finds a book with the hidden key inside within five seconds of entering the mansion's library. I strive to weave a plausible storyline where plot points seem to occur organically.
Sometimes, my story will spin out itself and the troubles faced by my characters come naturally out of prior situations, but it is when I find myself needing to arrive at plot point D while languishing at point B with no real sense of direction, that situations can seem contrived and have to be heavily edited if not axed at a later editing stage! I love to hear writers who find this process happens naturally for them, but I suspect that blood, sweat and tears are shed at some point in the story-writing process. It's never that easy!
In my case, I currently have Ethan needing to be caught in a situation he will not be able to escape from but where Holly will find him, unaware that her efforts to save him are futile. It is a situation they have learned other children have been caught up in, yet in their attempts to solve the problem the boy has become the latest victim. I have outlined the plot, sketching over this, and after writing the section when Holly realises where Ethan has gone, I have leapt a few chapters and am currently writing from the point where Holly has found him. I have no idea how he became trapped. Maybe, my weekend outing to Derbyshire with my dear Dad will inspire me. He knows the area inside out and is prepared to show me landscape features similar to those stumbled upon by my main characters. I'm hoping that walking in their footsteps, so to speak, will help the story evolve or maybe this will remain a problem for some time to come. For now I have no idea how I will get from A to C. B just is not happening for me yet.
I'm learning that I can't always write from beginning to end, as I have done previously, in fear of the story creaking and spluttering along with unnecessary fluff to move the reader along.
My writing style is starting to resemble building a tapestry, section by section, with no particular order, but in sections, with layers of colour being added to complement each other. This way, I'm finding that if I am struggling with the chronology of a story, particularly when more than one character is central to the story, I am writing one character's journey section, then perhaps flick to another section. However, this is within a detailed outline within which I've not yet worked out the cause and effect. A little messy at this stage, but the edit is where the picture becomes clear. (I hope!)
I write on my lap top chronologically, then as soon as the structure becomes more complicated, I focus on one line of the story, writing in my notebook, in seperate files on my laptop, on post-it notes and diary pages, then compile them each week as they find their way.
I'm not even sure I enjoy this rather fragmented framework as it is building, but it certainly allows me time and space to develop my plots and strengthen my characters' motivations behind their actions.
I love to see the full story emerge and the twists and turns finally come together, yet at this point it seems such a long way away.
Lorena suggests writing a very detailed synopsis of the story. When I have my first draft, I will certainly do this, in a bid to see the story outline in full. By sharing it with a few key readers, their responses will guide me on the next edit. Her guide to their responses should stand me in good stead:
      
If the reader says:                                                My next steps are to . . .

Is that it?                                                             Suspend disbelief and
                                                                            strengthen story
Give me a break!                                                Make more realistic,
                                                                            convincing
But what happens?                                             Get to the plot sooner

Hang on, but you said ...                                     Make story consistent

But what happened to ...                                     Tie up loose ends

Right. I'd better get back to Ethan - he's trapped deep below ground and time's running out!